Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop

Conflicts:
	webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsForIndividualGenerator.java

utilities/buildutils/src/edu/cornell/mannlib/vitro/utilities/testing/VitroTestRunListener.java

@@ -1,7 +1,7 @@
 /* $This file is distributed under the terms of the license in /doc/license.txt$ */
 
-package edu.cornell.mannlib.vitro.utilities.testing;
+package edu.cornell.mannlib.vitro.utilities.testing;
-
+
 import static edu.cornell.mannlib.vitro.utilities.testing.VitroTestRunner.ReportLevel.BRIEF;
 import static edu.cornell.mannlib.vitro.utilities.testing.VitroTestRunner.ReportLevel.FULL;
 import static edu.cornell.mannlib.vitro.utilities.testing.VitroTestRunner.ReportLevel.MORE;
@@ -20,327 +20,327 @@ import org.junit.runner.notification.Failure;
 import org.junit.runner.notification.RunListener;
 
 import edu.cornell.mannlib.vitro.utilities.testing.VitroTestRunner.ReportLevel;
-
+
-/**
+/**
- * Listen to events as they come from the JUnit test runner. The events from the
+ * Listen to events as they come from the JUnit test runner. The events from the
- * lifecycle methods are broken down into semantic chunks and executed. Three
+ * lifecycle methods are broken down into semantic chunks and executed. Three
- * levels of output are available.
+ * levels of output are available.
- * 
+ * 
- * On the surface, JUnit treats "failures" (failed assertions) the same as
+ * On the surface, JUnit treats "failures" (failed assertions) the same as
- * "errors" (unexpected exceptions). We're going to distinguish between them.
+ * "errors" (unexpected exceptions). We're going to distinguish between them.
- * 
+ * 
- * @author jeb228
+ * @author jeb228
- */
+ */
-public class VitroTestRunListener extends RunListener {
+public class VitroTestRunListener extends RunListener {
-	private final ReportLevel reportLevel;
+	private final ReportLevel reportLevel;
-
+
-	private int classCount;
+	private int classCount;
-	private int testsTotal;
+	private int testsTotal;
-	private int errorsTotal;
+	private int errorsTotal;
-	private int failuresTotal;
+	private int failuresTotal;
-	private int ignoresTotal;
+	private int ignoresTotal;
-	private long overallStartTime;
+	private long overallStartTime;
-
+
-	private Class<?> currentClass;
+	private Class<?> currentClass;
-	private int testsCurrentClass;
+	private int testsCurrentClass;
-	private int errorsCurrentClass;
+	private int errorsCurrentClass;
-	private int failuresCurrentClass;
+	private int failuresCurrentClass;
-	private int ignoresCurrentClass;
+	private int ignoresCurrentClass;
-	private long classStartTime;
+	private long classStartTime;
-
+
-	private String currentTest;
+	private String currentTest;
-	private boolean testHadError;
+	private boolean testHadError;
-	private boolean testFailed;
+	private boolean testFailed;
-	private boolean testIgnored;
+	private boolean testIgnored;
-	private long testStartTime;
+	private long testStartTime;
-
+
-	public VitroTestRunListener(ReportLevel reportLevel) {
+	public VitroTestRunListener(ReportLevel reportLevel) {
-		this.reportLevel = reportLevel;
+		this.reportLevel = reportLevel;
-	}
+	}
-
+
-	/** Did any of the tests fail or have errors? */
+	/** Did any of the tests fail or have errors? */
-	public boolean didEverythingPass() {
+	public boolean didEverythingPass() {
-		return (failuresTotal == 0) && (errorsTotal == 0);
+		return (failuresTotal == 0) && (errorsTotal == 0);
-	}
+	}
-
+
-	// -------------------------------------------------------------------------
+	// -------------------------------------------------------------------------
-	// Life-cycle methods that will be called by the test runner.
+	// Life-cycle methods that will be called by the test runner.
-	// -------------------------------------------------------------------------
+	// -------------------------------------------------------------------------
-
+
-	@Override
+	@Override
-	public void testRunStarted(Description description) throws Exception {
+	public void testRunStarted(Description description) throws Exception {
-		openTestRun();
+		openTestRun();
-		reportTestRunStart();
+		reportTestRunStart();
-	}
+	}
-
+
-	@Override
+	@Override
-	public void testStarted(Description description) throws Exception {
+	public void testStarted(Description description) throws Exception {
-		if (currentClass != description.getTestClass()) {
+		if (currentClass != description.getTestClass()) {
-			if (currentClass != null) {
+			if (currentClass != null) {
-				closeCurrentClass();
+				closeCurrentClass();
-				reportCurrentClass();
+				reportCurrentClass();
-			}
+			}
-
+
-			openCurrentClass(description);
+			openCurrentClass(description);
-			reportCurrentClassStart();
+			reportCurrentClassStart();
-		}
+		}
-
+
-		openCurrentTest(description);
+		openCurrentTest(description);
-	}
+	}
-
+
-	@Override
+	@Override
-	public void testAssumptionFailure(Failure failure) {
+	public void testAssumptionFailure(Failure failure) {
-		if (isError(failure)) {
+		if (isError(failure)) {
-			testHadError = true;
+			testHadError = true;
-			reportError(failure);
+			reportError(failure);
-		} else {
+		} else {
-			testFailed = true;
+			testFailed = true;
-			reportFailure(failure);
+			reportFailure(failure);
-		}
+		}
-	}
+	}
-
+
-	@Override
+	@Override
-	public void testFailure(Failure failure) throws Exception {
+	public void testFailure(Failure failure) throws Exception {
-		if (isError(failure)) {
+		if (isError(failure)) {
-			testHadError = true;
+			testHadError = true;
-			reportError(failure);
+			reportError(failure);
-		} else {
+		} else {
-			testFailed = true;
+			testFailed = true;
-			reportFailure(failure);
+			reportFailure(failure);
-		}
+		}
-	}
+	}
-
+
-	@Override
+	@Override
-	public void testFinished(Description description) throws Exception {
+	public void testFinished(Description description) throws Exception {
-		closeCurrentTest();
+		closeCurrentTest();
-		reportCurrentTest();
+		reportCurrentTest();
-	}
+	}
-
+
-	@Override
+	@Override
-	public void testIgnored(Description description) throws Exception {
+	public void testIgnored(Description description) throws Exception {
-		testStarted(description);
+		testStarted(description);
-		testIgnored = true;
+		testIgnored = true;
-		testFinished(description);
+		testFinished(description);
-	}
+	}
-
+
-	@Override
+	@Override
-	public void testRunFinished(Result result) throws Exception {
+	public void testRunFinished(Result result) throws Exception {
-		if (currentClass != null) {
+		if (currentClass != null) {
-			closeCurrentClass();
+			closeCurrentClass();
-			reportCurrentClass();
+			reportCurrentClass();
-		}
+		}
-		closeTestRun();
+		closeTestRun();
-		reportTestRun();
+		reportTestRun();
-		System.out.println();
+		System.out.println();
-	}
+	}
-
+
-	// -------------------------------------------------------------------------
+	// -------------------------------------------------------------------------
-	// Handling the logical events.
+	// Handling the logical events.
-	// -------------------------------------------------------------------------
+	// -------------------------------------------------------------------------
-
+
-	private void openTestRun() {
+	private void openTestRun() {
-		overallStartTime = System.currentTimeMillis();
+		overallStartTime = System.currentTimeMillis();
-	}
+	}
-
+
-	private void closeTestRun() {
+	private void closeTestRun() {
-		// Nothing to close.
+		// Nothing to close.
-	}
+	}
-
+
-	private void reportTestRunStart() {
+	private void reportTestRunStart() {
-		if (reportLevel == FULL) {
+		if (reportLevel == FULL) {
-			System.out
+			System.out
-					.println("Starting test run at " + time(overallStartTime));
+					.println("Starting test run at " + time(overallStartTime));
-			System.out.println();
+			System.out.println();
-		}
+		}
-
+
-		if (reportLevel == MORE) {
+		if (reportLevel == MORE) {
-			System.out
+			System.out
-					.println("Starting test run at " + time(overallStartTime));
+					.println("Starting test run at " + time(overallStartTime));
-			System.out.println();
+			System.out.println();
-			System.out.println("Tests Pass Error Fail Ignore Seconds");
+			System.out.println("Tests Pass Error Fail Ignore Seconds");
-		}
+		}
-	}
+	}
-
+
-	private void reportTestRun() {
+	private void reportTestRun() {
-		int successes = testsTotal - errorsTotal - failuresTotal - ignoresTotal;
+		int successes = testsTotal - errorsTotal - failuresTotal - ignoresTotal;
-
+
-		if (reportLevel != BRIEF) {
+		if (reportLevel != BRIEF) {
-			System.out.println();
+			System.out.println();
-		}
+		}
-
+
-		System.out.format(
+		System.out.format(
-				"Tests Pass Error Fail Ignore Seconds  TOTAL (%d classes)\n",
+				"Tests Pass Error Fail Ignore Seconds  TOTAL (%d classes)\n",
-				classCount);
+				classCount);
-		System.out.format(" %4d %4d  %4d %4d  %4d  %6s\n", testsTotal,
+		System.out.format(" %4d %4d  %4d %4d  %4d  %6s\n", testsTotal,
-				successes, errorsTotal, failuresTotal, ignoresTotal,
+				successes, errorsTotal, failuresTotal, ignoresTotal,
-				elapsed(overallStartTime));
+				elapsed(overallStartTime));
-
+
-		if (reportLevel != BRIEF) {
+		if (reportLevel != BRIEF) {
-			System.out.println("Ending test run at "
+			System.out.println("Ending test run at "
-					+ time(System.currentTimeMillis()));
+					+ time(System.currentTimeMillis()));
-		}
+		}
-	}
+	}
-
+
-	private void openCurrentClass(Description description) {
+	private void openCurrentClass(Description description) {
-		currentClass = description.getTestClass();
+		currentClass = description.getTestClass();
-		classStartTime = System.currentTimeMillis();
+		classStartTime = System.currentTimeMillis();
-		testsCurrentClass = 0;
+		testsCurrentClass = 0;
-		errorsCurrentClass = 0;
+		errorsCurrentClass = 0;
-		failuresCurrentClass = 0;
+		failuresCurrentClass = 0;
-		ignoresCurrentClass = 0;
+		ignoresCurrentClass = 0;
-	}
+	}
-
+
-	private void closeCurrentClass() {
+	private void closeCurrentClass() {
-		classCount++;
+		classCount++;
-		testsTotal += testsCurrentClass;
+		testsTotal += testsCurrentClass;
-		errorsTotal += errorsCurrentClass;
+		errorsTotal += errorsCurrentClass;
-		failuresTotal += failuresCurrentClass;
+		failuresTotal += failuresCurrentClass;
-		ignoresTotal += ignoresCurrentClass;
+		ignoresTotal += ignoresCurrentClass;
-	}
+	}
-
+
-	private void reportCurrentClassStart() {
+	private void reportCurrentClassStart() {
-		if (reportLevel == FULL) {
+		if (reportLevel == FULL) {
-			System.out.format("Tests Pass Error Fail Ignore Seconds  %s\n",
+			System.out.format("Tests Pass Error Fail Ignore Seconds  %s\n",
-					currentClass.getName());
+					currentClass.getName());
-		}
+		}
-	}
+	}
-
+
-	private void reportCurrentClass() {
+	private void reportCurrentClass() {
-		int successes = testsCurrentClass - errorsCurrentClass
+		int successes = testsCurrentClass - errorsCurrentClass
-				- failuresCurrentClass - ignoresCurrentClass;
+				- failuresCurrentClass - ignoresCurrentClass;
-		if (reportLevel == MORE) {
+		if (reportLevel == MORE) {
-			System.out.format(" %4d %4d  %4d %4d  %4d  %6s %s\n",
+			System.out.format(" %4d %4d  %4d %4d  %4d  %6s %s\n",
-					testsCurrentClass, successes, errorsCurrentClass,
+					testsCurrentClass, successes, errorsCurrentClass,
-					failuresCurrentClass, ignoresCurrentClass,
+					failuresCurrentClass, ignoresCurrentClass,
-					elapsed(classStartTime), currentClass.getSimpleName());
+					elapsed(classStartTime), currentClass.getSimpleName());
-		}
+		}
-		if (reportLevel == FULL) {
+		if (reportLevel == FULL) {
-			System.out.println("-----------------------------------");
+			System.out.println("-----------------------------------");
-			System.out.format(" %4d %4d  %4d %4d  %4d  %6s\n",
+			System.out.format(" %4d %4d  %4d %4d  %4d  %6s\n",
-					testsCurrentClass, successes, errorsCurrentClass,
+					testsCurrentClass, successes, errorsCurrentClass,
-					failuresCurrentClass, ignoresCurrentClass,
+					failuresCurrentClass, ignoresCurrentClass,
-					elapsed(classStartTime));
+					elapsed(classStartTime));
-			System.out.println();
+			System.out.println();
-		}
+		}
-	}
+	}
-
+
-	private void openCurrentTest(Description description) {
+	private void openCurrentTest(Description description) {
-		currentTest = description.getMethodName();
+		currentTest = description.getMethodName();
-		testHadError = false;
+		testHadError = false;
-		testFailed = false;
+		testFailed = false;
-		testIgnored = false;
+		testIgnored = false;
-		testStartTime = System.currentTimeMillis();
+		testStartTime = System.currentTimeMillis();
-	}
+	}
-
+
-	private void closeCurrentTest() {
+	private void closeCurrentTest() {
-		if (testHadError) {
+		if (testHadError) {
-			errorsCurrentClass++;
+			errorsCurrentClass++;
-		}
+		}
-		if (testFailed) {
+		if (testFailed) {
-			failuresCurrentClass++;
+			failuresCurrentClass++;
-		}
+		}
-		if (testIgnored) {
+		if (testIgnored) {
-			ignoresCurrentClass++;
+			ignoresCurrentClass++;
-		}
+		}
-		testsCurrentClass++;
+		testsCurrentClass++;
-	}
+	}
-
+
-	private boolean isError(Failure failure) {
+	private boolean isError(Failure failure) {
-		Throwable throwable = failure.getException();
+		Throwable throwable = failure.getException();
-		return (throwable != null) && !(throwable instanceof AssertionError);
+		return (throwable != null) && !(throwable instanceof AssertionError);
-	}
+	}
-
+
-	private void reportError(Failure error) {
+	private void reportError(Failure error) {
-		Description description = error.getDescription();
+		Description description = error.getDescription();
-		String methodName = description.getMethodName();
+		String methodName = description.getMethodName();
-		String className = description.getTestClass().getName();
+		String className = description.getTestClass().getName();
-		String message = error.getMessage();
+		String message = error.getMessage();
-		System.out.format("EXCEPTION:   test %s() in %s: %s\n",
+		System.out.format("EXCEPTION:   test %s() in %s: %s\n",
-				methodName, className, message);
+				methodName, className, message);
-		System.out.println(formatStackTrace(error.getException()));
+		System.out.println(formatStackTrace(error.getException()));
-	}
+	}
-
+
-	private void reportFailure(Failure failure) {
+	private void reportFailure(Failure failure) {
-		Description description = failure.getDescription();
+		Description description = failure.getDescription();
-		String methodName = description.getMethodName();
+		String methodName = description.getMethodName();
-		String className = description.getTestClass().getName();
+		String className = description.getTestClass().getName();
-		String message = failure.getMessage();
+		String message = failure.getMessage();
-		System.out.format("TEST FAILED: test %s() in %s: %s\n", methodName,
+		System.out.format("TEST FAILED: test %s() in %s: %s\n", methodName,
-				className, message);
+				className, message);
-	}
+	}
-
+
-	private void reportCurrentTest() {
+	private void reportCurrentTest() {
-		if (reportLevel == FULL) {
+		if (reportLevel == FULL) {
-			char passFlag = (testIgnored | testFailed | testHadError) ? ' '
+			char passFlag = (testIgnored | testFailed | testHadError) ? ' '
-					: '1';
+					: '1';
-			char errorFlag = testHadError ? '1' : ' ';
+			char errorFlag = testHadError ? '1' : ' ';
-			char failFlag = testFailed ? '1' : ' ';
+			char failFlag = testFailed ? '1' : ' ';
-			char ignoreFlag = testIgnored ? '1' : ' ';
+			char ignoreFlag = testIgnored ? '1' : ' ';
-			System.out.format(
+			System.out.format(
-					"         %c     %c    %c      %c %6s        %s()\n",
+					"         %c     %c    %c      %c %6s        %s()\n",
-					passFlag, errorFlag, failFlag, ignoreFlag,
+					passFlag, errorFlag, failFlag, ignoreFlag,
-					elapsed(testStartTime), currentTest);
+					elapsed(testStartTime), currentTest);
-		}
+		}
-	}
+	}
-
+
-	// -------------------------------------------------------------------------
+	// -------------------------------------------------------------------------
-	// Formatting methods.
+	// Formatting methods.
-	// -------------------------------------------------------------------------
+	// -------------------------------------------------------------------------
-
+
-	private final SimpleDateFormat formatter = new SimpleDateFormat(
+	private final SimpleDateFormat formatter = new SimpleDateFormat(
-			"HH:mm:ss 'on' MMM dd, yyyy");
+			"HH:mm:ss 'on' MMM dd, yyyy");
-
+
-	private String time(long time) {
+	private String time(long time) {
-		return formatter.format(new Date(time));
+		return formatter.format(new Date(time));
-	}
+	}
-
+
-	/** Show elapsed time in 6 columns. */
+	/** Show elapsed time in 6 columns. */
-	private String elapsed(long start) {
+	private String elapsed(long start) {
-		long interval = System.currentTimeMillis() - start;
+		long interval = System.currentTimeMillis() - start;
-		return String.format("%6.2f", ((float) interval) / 1000.0);
+		return String.format("%6.2f", ((float) interval) / 1000.0);
-	}
+	}
-
+
-	/**
+	/**
-	 * Trim the stack trace: don't show the line saying "23 more", and don't
+	 * Trim the stack trace: don't show the line saying "23 more", and don't
-	 * show the lines about org.junit or java.lang.reflect or sun.reflect.
+	 * show the lines about org.junit or java.lang.reflect or sun.reflect.
-	 * 
+	 * 
-	 * Once we hit some "client code", we won't trim any futher lines even if
+	 * Once we hit some "client code", we won't trim any futher lines even if
-	 * they belong to org.junit, or the others.
+	 * they belong to org.junit, or the others.
-	 * 
+	 * 
-	 * If we have nested exceptions, the process repeats for each "Caused by"
+	 * If we have nested exceptions, the process repeats for each "Caused by"
-	 * section.
+	 * section.
-	 */
+	 */
-	private String formatStackTrace(Throwable throwable) {
+	private String formatStackTrace(Throwable throwable) {
-		StringWriter w = new StringWriter();
+		StringWriter w = new StringWriter();
-		throwable.printStackTrace(new PrintWriter(w));
+		throwable.printStackTrace(new PrintWriter(w));
-		String[] lineArray = w.toString().split("\\n");
+		String[] lineArray = w.toString().split("\\n");
-		List<String> lines = new ArrayList<String>(Arrays.asList(lineArray));
+		List<String> lines = new ArrayList<String>(Arrays.asList(lineArray));
-
+
-		boolean removing = true;
+		boolean removing = true;
-		for (int i = lines.size() - 1; i > 0; i--) {
+		for (int i = lines.size() - 1; i > 0; i--) {
-			String line = lines.get(i);
+			String line = lines.get(i);
-			if (removing) {
+			if (removing) {
-				if (line.matches("\\s*[\\.\\s\\d]+more\\s*")
+				if (line.matches("\\s*[\\.\\s\\d]+more\\s*")
-						|| line.contains("at "
+						|| line.contains("at "
-								+ VitroTestRunner.class.getName())
+								+ VitroTestRunner.class.getName())
-						|| line.contains("at org.junit.")
+						|| line.contains("at org.junit.")
-						|| line.contains("at java.lang.reflect.")
+						|| line.contains("at java.lang.reflect.")
-						|| line.contains("at sun.reflect.")) {
+						|| line.contains("at sun.reflect.")) {
-					lines.remove(line);
+					lines.remove(line);
-				} else {
+				} else {
-					removing = false;
+					removing = false;
-				}
+				}
-			} else {
+			} else {
-				if (line.contains("Caused by: ")) {
+				if (line.contains("Caused by: ")) {
-					removing = true;
+					removing = true;
-				}
+				}
-			}
+			}
-		}
+		}
-
+
-		StringBuilder result = new StringBuilder();
+		StringBuilder result = new StringBuilder();
-		for (String line : lines) {
+		for (String line : lines) {
-			result.append(line).append('\n');
+			result.append(line).append('\n');
-		}
+		}
-		return result.toString().trim();
+		return result.toString().trim();
-	}
+	}
-}
+}

webapp/rdf/displayTbox/everytime/displayTBOX.n3

@@ -35,7 +35,7 @@ display:InternalClassesPage a owl:Class .
 display:DataGetter a owl:Class .  
 
 display:RequiredAction a owl:Class ;
-    rdfs:comment "Represents a action that may need authorization to perform.".
+    rdfs:comment "Represents a action that may need authorization to perform." .
 
 <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter>
     a owl:Class ;
@@ -55,11 +55,11 @@ display:RequiredAction a owl:Class ;
 
 <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData>
     a owl:Class ;
-    rdfs:comment "A data getter for a VClassGroup page".
+    rdfs:comment "A data getter for a VClassGroup page" .
 
 <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.FixedHTMLDataGetter>
     a owl:Class ;
-    rdfs:comment "A data getter for a Fixed piece of HTML stored in RDF".
+    rdfs:comment "A data getter for a Fixed piece of HTML stored in RDF" .
 
 <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter>
     a owl:Class .

webapp/src/edu/cornell/mannlib/vedit/validator/impl/UrlValidator.java

@@ -2,28 +2,37 @@
 
 package edu.cornell.mannlib.vedit.validator.impl;
 
-import edu.cornell.mannlib.vedit.validator.Validator;
+import java.util.Iterator;
+
+import com.hp.hpl.jena.iri.IRI;
+import com.hp.hpl.jena.iri.IRIFactory;
+import com.hp.hpl.jena.iri.Violation;
+
 import edu.cornell.mannlib.vedit.validator.ValidationObject;
-import java.util.regex.*;
+import edu.cornell.mannlib.vedit.validator.Validator;
 
 public class UrlValidator implements Validator {
 
     public ValidationObject validate (Object obj) throws IllegalArgumentException {
 
         ValidationObject vo = new ValidationObject();
-        String theString = null;
 
         if (!(obj instanceof String)){
             throw new IllegalArgumentException("Expected instance of String");
         }
 
-        Pattern pat = Pattern.compile("[a-z]{3,5}*://.*\\.[a-z]{2,4}");
+        IRIFactory factory = IRIFactory.jenaImplementation();
-        Matcher mat = pat.matcher(theString);
+        IRI iri = factory.create((String) obj);
-        if (mat.matches()){
+        if (iri.hasViolation(false) ) {
-            vo.setValid(true);
+            String errorStr = "";
-        } else {
+            Iterator<Violation> violIt = iri.violations(false);
+            while(violIt.hasNext()) {
+                errorStr += violIt.next().getShortMessage() + "  ";
+            }
             vo.setValid(false);
-            vo.setMessage("Please enter a valid URL");
+            vo.setMessage("Please enter a valid URL.  " + errorStr);
+        } else {
+            vo.setValid(true);
         }
 
         vo.setValidatedObject(obj);

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/DisplayByRolePermission.java

@@ -16,6 +16,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAct
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Is the user authorized to display properties that are marked as restricted to
@@ -82,7 +83,7 @@ public class DisplayByRolePermission extends Permission {
 	 */
 	private boolean isAuthorized(DisplayDataProperty action) {
 		String predicateUri = action.getDataProperty().getURI();
-		return canDisplayPredicate(predicateUri);
+		return canDisplayPredicate(new Property(predicateUri));
 	}
 
 	/**
@@ -90,8 +91,7 @@ public class DisplayByRolePermission extends Permission {
 	 * predicate.
 	 */
 	private boolean isAuthorized(DisplayObjectProperty action) {
-		String predicateUri = action.getObjectProperty().getURI();
+		return canDisplayPredicate(action.getObjectProperty());
-		return canDisplayPredicate(predicateUri);
 	}
 
 	/**
@@ -103,7 +103,7 @@ public class DisplayByRolePermission extends Permission {
 		String subjectUri = stmt.getIndividualURI();
 		String predicateUri = stmt.getDatapropURI();
 		return canDisplayResource(subjectUri)
-				&& canDisplayPredicate(predicateUri);
+				&& canDisplayPredicate(new Property(predicateUri));
 	}
 
 	/**
@@ -113,12 +113,10 @@ public class DisplayByRolePermission extends Permission {
 	private boolean isAuthorized(DisplayObjectPropertyStatement action) {
 		ObjectPropertyStatement stmt = action.getObjectPropertyStatement();
 		String subjectUri = stmt.getSubjectURI();
-		String predicateUri = stmt.getPropertyURI();
+		Property predicate = stmt.getProperty(); 
-		String rangeUri = (stmt.getProperty() == null) ? null 
-		        : stmt.getProperty().getRangeVClassURI();
 		String objectUri = stmt.getObjectURI();
 		return canDisplayResource(subjectUri)
-				&& canDisplayPredicate(predicateUri, rangeUri)
+				&& canDisplayPredicate(predicate)
 				&& canDisplayResource(objectUri);
 	}
 
@@ -126,14 +124,10 @@ public class DisplayByRolePermission extends Permission {
 		return PropertyRestrictionPolicyHelper.getBean(ctx).canDisplayResource(
 				resourceUri, this.roleLevel);
 	}
-	
-	private boolean canDisplayPredicate(String predicateUri) {
-	    return canDisplayPredicate(predicateUri, null);
-	}
 
-	private boolean canDisplayPredicate(String predicateUri, String rangeUri) {
+	private boolean canDisplayPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx)
-				.canDisplayPredicate(predicateUri, rangeUri, this.roleLevel);
+				.canDisplayPredicate(predicate, this.roleLevel);
 	}
 
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/EditByRolePermission.java

@@ -12,6 +12,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAct
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractDataPropertyStatementAction;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractObjectPropertyStatementAction;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Is the user authorized to edit properties that are marked as restricted to a
@@ -78,9 +79,9 @@ public class EditByRolePermission extends Permission {
 	 */
 	private boolean isAuthorized(AbstractDataPropertyStatementAction action) {
 		String subjectUri = action.getSubjectUri();
-		String predicateUri = action.getPredicateUri();
+		Property predicate = action.getPredicate();
 		return canModifyResource(subjectUri)
-				&& canModifyPredicate(predicateUri);
+				&& canModifyPredicate(predicate);
 	}
 
 	/**
@@ -89,10 +90,10 @@ public class EditByRolePermission extends Permission {
 	 */
 	private boolean isAuthorized(AbstractObjectPropertyStatementAction action) {
 		String subjectUri = action.getSubjectUri();
-		String predicateUri = action.getPredicateUri();
+		Property predicate = action.getPredicate();
 		String objectUri = action.getObjectUri();
 		return canModifyResource(subjectUri)
-				&& canModifyPredicate(predicateUri)
+				&& canModifyPredicate(predicate)
 				&& canModifyResource(objectUri);
 	}
 
@@ -101,9 +102,9 @@ public class EditByRolePermission extends Permission {
 				resourceUri, roleLevel);
 	}
 
-	private boolean canModifyPredicate(String predicateUri) {
+	private boolean canModifyPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx).canModifyPredicate(
-				predicateUri, roleLevel);
+				predicate, roleLevel);
 	}
 
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/BaseSelfEditingPolicy.java

@@ -8,6 +8,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.policy.bean.PropertyRestrictionPoli
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.Authorization;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.PolicyDecision;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A base class with utility methods for policies involving self-editing.
@@ -26,9 +27,9 @@ public abstract class BaseSelfEditingPolicy {
 				uri, roleLevel);
 	}
 
-	protected boolean canModifyPredicate(String uri) {
+	protected boolean canModifyPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx).canModifyPredicate(
-				uri, roleLevel);
+				predicate, roleLevel);
 	}
 
 	protected PolicyDecision cantModifyResource(String uri) {
@@ -36,9 +37,9 @@ public abstract class BaseSelfEditingPolicy {
 				+ uri);
 	}
 
-	protected PolicyDecision cantModifyPredicate(String uri) {
+	protected PolicyDecision cantModifyPredicate(Property predicate) {
 		return inconclusiveDecision("No access to admin predicates; cannot modify "
-				+ uri);
+				+ predicate.getURI());
 	}
 
 	protected PolicyDecision userNotAuthorizedToStatement() {

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/DisplayRestrictedDataToSelfPolicy.java

@@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAct
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Permit display of various data if it relates to the user's associated
@@ -92,14 +93,14 @@ public class DisplayRestrictedDataToSelfPolicy implements PolicyIface {
 			Collection<String> individuals) {
 		DataPropertyStatement stmt = action.getDataPropertyStatement();
 		String subjectUri = stmt.getIndividualURI();
-		String predicateUri = stmt.getDatapropURI();
+		Property predicate = new Property(stmt.getDatapropURI());
-		if (canDisplayResource(subjectUri) && canDisplayPredicate(predicateUri)
+		if (canDisplayResource(subjectUri) && canDisplayPredicate(predicate)
 				&& isAboutAssociatedIndividual(individuals, stmt)) {
 			return authorized("user may view DataPropertyStatement "
-					+ subjectUri + " ==> " + predicateUri);
+					+ subjectUri + " ==> " + predicate.getURI());
 		} else {
 			return defaultDecision("user may not view DataPropertyStatement "
-					+ subjectUri + " ==> " + predicateUri);
+					+ subjectUri + " ==> " + predicate.getURI());
 		}
 	}
 
@@ -115,7 +116,8 @@ public class DisplayRestrictedDataToSelfPolicy implements PolicyIface {
 		String subjectUri = stmt.getSubjectURI();
 		String predicateUri = stmt.getPropertyURI();
 		String objectUri = stmt.getObjectURI();
-		if (canDisplayResource(subjectUri) && canDisplayPredicate(predicateUri)
+		if (canDisplayResource(subjectUri) && canDisplayPredicate(new Property
+		                (predicateUri))
 				&& canDisplayResource(objectUri)
 				&& isAboutAssociatedIndividual(individuals, stmt)) {
 			return authorized("user may view ObjectPropertyStatement "
@@ -143,9 +145,9 @@ public class DisplayRestrictedDataToSelfPolicy implements PolicyIface {
 				uri, RoleLevel.SELF);
 	}
 
-	private boolean canDisplayPredicate(String uri) {
+	private boolean canDisplayPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx)
-				.canDisplayPredicate(uri, RoleLevel.SELF);
+				.canDisplayPredicate(predicate, RoleLevel.SELF);
 	}
 
 	private boolean isAboutAssociatedIndividual(Collection<String> selves,

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/PermissionsPolicy.java

@@ -35,6 +35,8 @@ public class PermissionsPolicy implements PolicyIface {
 				log.debug("Permission " + p + " approves request " + whatToAuth);
 				return new BasicPolicyDecision(Authorization.AUTHORIZED,
 						"PermissionsPolicy: approved by " + p);
+			} else {
+			    log.trace("Permission " + p + " denies request " + whatToAuth);
 			}
 		}
 		log.debug("No permission will approve " + whatToAuth);

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/PolicyHelper.java

@@ -122,7 +122,8 @@ public class PolicyHelper {
 		}
 
 		Resource subject = stmt.getSubject();
-		Property predicate = stmt.getPredicate();
+		edu.cornell.mannlib.vitro.webapp.beans.Property predicate = 
+		        new edu.cornell.mannlib.vitro.webapp.beans.Property(stmt.getPredicate().getURI());
 		RDFNode objectNode = stmt.getObject();
 		if ((subject == null) || (predicate == null) || (objectNode == null)) {
 			return false;
@@ -131,7 +132,7 @@ public class PolicyHelper {
 		RequestedAction action;
 		if (objectNode.isResource()) {
 			action = new AddObjectPropertyStatement(modelToBeModified,
-					subject.getURI(), predicate.getURI(), objectNode
+					subject.getURI(), predicate, objectNode
 							.asResource().getURI());
 		} else {
 			action = new AddDataPropertyStatement(modelToBeModified,
@@ -153,7 +154,9 @@ public class PolicyHelper {
 		}
 
 		Resource subject = stmt.getSubject();
-		Property predicate = stmt.getPredicate();
+		edu.cornell.mannlib.vitro.webapp.beans.Property predicate = 
+		        new edu.cornell.mannlib.vitro.webapp.beans.Property();
+		predicate.setURI(stmt.getPredicate().getURI());
 		RDFNode objectNode = stmt.getObject();
 		if ((subject == null) || (predicate == null) || (objectNode == null)) {
 			return false;
@@ -162,7 +165,7 @@ public class PolicyHelper {
 		RequestedAction action;
 		if (objectNode.isResource()) {
 			action = new DropObjectPropertyStatement(modelToBeModified,
-					subject.getURI(), predicate.getURI(), objectNode
+					subject.getURI(), predicate, objectNode
 							.asResource().getURI());
 		} else {
 			action = new DropDataPropertyStatement(modelToBeModified,

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/SelfEditingPolicy.java

@@ -16,6 +16,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractDa
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractObjectPropertyStatementAction;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.resource.AbstractResourceAction;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Policy to use for Vivo Self-Editing based on NetId for use at Cornell. All
@@ -69,7 +70,7 @@ public class SelfEditingPolicy extends BaseSelfEditingPolicy implements
 	private PolicyDecision isAuthorizedForObjectPropertyAction(
 			List<String> userUris, AbstractObjectPropertyStatementAction action) {
 		String subject = action.getSubjectUri();
-		String predicate = action.getPredicateUri();
+		Property predicate = action.getPredicate();
 		String object = action.getObjectUri();
 
 		if (!canModifyResource(subject)) {
@@ -96,7 +97,7 @@ public class SelfEditingPolicy extends BaseSelfEditingPolicy implements
 	private PolicyDecision isAuthorizedForDataPropertyAction(
 			List<String> userUris, AbstractDataPropertyStatementAction action) {
 		String subject = action.getSubjectUri();
-		String predicate = action.getPredicateUri();
+		Property predicate = action.getPredicate();
 
 		if (!canModifyResource(subject)) {
 			return cantModifyResource(subject);

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelper.java

@@ -7,6 +7,7 @@ import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 
 import javax.servlet.ServletContext;
@@ -17,6 +18,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -24,18 +26,23 @@ 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.Model;
-import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.rdf.model.impl.Util;
+import com.hp.hpl.jena.sdb.util.Pair;
 import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
+import edu.cornell.mannlib.vitro.webapp.utils.ApplicationConfigurationOntologyUtils;
 
 /**
  * Assists the role-based policies in determining whether a property or resource
@@ -108,17 +115,22 @@ public class PropertyRestrictionPolicyHelper {
 	                                                         Model displayModel) {
 	    
 	    
-		Map<String, RoleLevel> displayThresholdMap = new HashMap<String, RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> displayThresholdMap = 
-		Map<String, RoleLevel> modifyThresholdMap = new HashMap<String, RoleLevel>();
+		        new HashMap<Pair<String, Pair<String,String>>, RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> modifyThresholdMap = 
+		        new HashMap<Pair<String, Pair<String,String>>, RoleLevel>();
+		
+		OntModel union = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
+		        ModelFactory.createUnion(displayModel, model));
+
+
+		populateThresholdMap(union, displayThresholdMap,
+				VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT);
+		populateThresholdMap(
+				union,
+				modifyThresholdMap,
+				VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT);
 
-		if (model != null) {
-			populateThresholdMap(model, displayThresholdMap,
-					VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT);
-			populateThresholdMap(
-					model,
-					modifyThresholdMap,
-					VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT);
-		}
 
 		PropertyRestrictionPolicyHelper bean = new PropertyRestrictionPolicyHelper(
 				PROHIBITED_NAMESPACES, PERMITTED_EXCEPTIONS,
@@ -127,29 +139,85 @@ public class PropertyRestrictionPolicyHelper {
 		return bean;
 	}
 
+	private RoleLevel getModifyThreshold(Property property) {
+	    return getThreshold(property, modifyThresholdMap);
+	}
+	
+	private RoleLevel getThreshold(Property property, 
+	                               Map<Pair<String, Pair<String,String>>, RoleLevel> 
+	                                       thresholdMap) {
+	    if (property.getURI() == null) {
+	        return RoleLevel.NOBODY;
+	    }
+	    RoleLevel roleLevel = getRoleLevelFromMap(
+	            property.getDomainVClassURI(), property.getURI(), 
+	                    property.getRangeVClassURI(), thresholdMap);
+	    if (roleLevel == null) {
+	        roleLevel = getRoleLevelFromMap(
+	                OWL.Thing.getURI(), property.getURI(), OWL.Thing.getURI(),
+	                        thresholdMap);
+	    }
+	    return roleLevel;
+	}
+	
+	private RoleLevel getRoleLevelFromMap(String domainURI, 
+	                                      String predicateURI, 
+	                                      String rangeURI,
+	                                      Map<Pair<String, Pair<String,String>>, 
+	                                              RoleLevel> map) {
+	    return map.get(
+                new Pair<String, Pair<String,String>>(
+                        domainURI, new Pair<String,String>(
+                                predicateURI, rangeURI)));
+	}
+	
 	/**
 	 * Find all the resources that possess this property, and map the resource
 	 * URI to the required RoleLevel.
 	 */
 	private static void populateThresholdMap(OntModel model,
-			Map<String, RoleLevel> map, String propertyUri) {
+			Map<Pair<String,Pair<String,String>>, RoleLevel> map, String propertyUri) {
 		model.enterCriticalSection(Lock.READ);
 		try {
-			Property property = model.getProperty(propertyUri);
+		    com.hp.hpl.jena.rdf.model.Property property = model.getProperty(propertyUri);
 			StmtIterator stmts = model.listStatements((Resource) null,
 					property, (Resource) null);
-			while (stmts.hasNext()) {
+			try {
-				Statement stmt = stmts.next();
+    			while (stmts.hasNext()) {
-				Resource subject = stmt.getSubject();
+    				Statement stmt = stmts.next();
-				RDFNode objectNode = stmt.getObject();
+    				Resource subject = stmt.getSubject();
-				if ((subject == null) || (!(objectNode instanceof Resource))) {
+    				RDFNode objectNode = stmt.getObject();
-					continue;
+    				if ((subject == null) || (!(objectNode instanceof Resource))) {
-				}
+    					continue;
-				Resource object = (Resource) objectNode;
+    				}
-				RoleLevel role = RoleLevel.getRoleByUri(object.getURI());
+    				Resource object = (Resource) objectNode;
-				map.put(subject.getURI(), role);
+    				RoleLevel role = RoleLevel.getRoleByUri(object.getURI());
+    				map.put(new Pair<String,Pair<String,String>>(
+    				        OWL.Thing.getURI(), new Pair<String,String>(
+    				                subject.getURI(), OWL.Thing.getURI())), role);
+    			} 
+			} finally {
+	            stmts.close();			    
 			}
-			stmts.close();
+            List<ObjectProperty> fauxOps = ApplicationConfigurationOntologyUtils
+                    .getAdditionalFauxSubproperties(null, null, model, model);
+            for (ObjectProperty faux : fauxOps) {
+                RoleLevel role = null;
+                if(VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT
+                        .equals(propertyUri)) {
+                    role = faux.getProhibitedFromUpdateBelowRoleLevel();
+                } else if (VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT
+                        .equals(propertyUri)) {
+                    role = faux.getHiddenFromDisplayBelowRoleLevel();
+                }
+                if (role != null) {
+                    log.debug("Putting D:" + faux.getDomainVClassURI() + " P:" + faux.getURI() + " R:" + faux.getRangeVClassURI() + " ==> L:" + role);
+                    map.put(new Pair<String,Pair<String,String>>(
+                            faux.getDomainVClassURI(), new Pair<String,String>(
+                                    faux.getURI(), faux.getRangeVClassURI())), role);
+                }
+            }
+
 		} finally {
 			model.leaveCriticalSection();
 		}
@@ -175,15 +243,14 @@ public class PropertyRestrictionPolicyHelper {
 	 * These URIs can be displayed only if the user's role is at least as high
 	 * as the threshold role.
 	 */
-	private final Map<String, RoleLevel> displayThresholdMap;
+	private final Map<Pair<String, Pair<String,String>>, RoleLevel> displayThresholdMap;
 
 	/**
 	 * These URIs can be modified only if the user's role is at least as high as
 	 * the threshold role.
 	 */
-	private final Map<String, RoleLevel> modifyThresholdMap;
+	private final Map<Pair<String, Pair<String,String>>, RoleLevel> modifyThresholdMap;
 	
-	private final Model displayModel;
 
 	/**
 	 * Store unmodifiable versions of the inputs.
@@ -194,14 +261,15 @@ public class PropertyRestrictionPolicyHelper {
 	protected PropertyRestrictionPolicyHelper(
 			Collection<String> modifyProhibitedNamespaces,
 			Collection<String> modifyExceptionsAllowedUris,
-			Map<String, RoleLevel> displayThresholdMap,
+			Map<Pair<String, Pair<String,String>>, RoleLevel> displayThresholdMap,
-			Map<String, RoleLevel> modifyThresholdMap,
+			Map<Pair<String, Pair<String,String>>, RoleLevel> modifyThresholdMap,
 			Model displayModel) {
 		this.modifyProhibitedNamespaces = unmodifiable(modifyProhibitedNamespaces);
 		this.modifyExceptionsAllowedUris = unmodifiable(modifyExceptionsAllowedUris);
-		this.displayThresholdMap = unmodifiable(displayThresholdMap);
+		this.displayThresholdMap = displayThresholdMap;
-		this.modifyThresholdMap = unmodifiable(modifyThresholdMap);
+		this.modifyThresholdMap = modifyThresholdMap;
-		this.displayModel = displayModel;
+//	    this.displayThresholdMap = unmodifiable(displayThresholdMap);
+//	    this.modifyThresholdMap = unmodifiable(modifyThresholdMap);
 
 		if (log.isDebugEnabled()) {
 			log.debug("prohibited: " + this.modifyProhibitedNamespaces);
@@ -219,6 +287,7 @@ public class PropertyRestrictionPolicyHelper {
 		}
 	}
 
+	@SuppressWarnings("unused")
 	private Map<String, RoleLevel> unmodifiable(Map<String, RoleLevel> raw) {
 		if (raw == null) {
 			return Collections.emptyMap();
@@ -271,83 +340,34 @@ public class PropertyRestrictionPolicyHelper {
 		log.debug("can modify resource '" + resourceUri + "'");
 		return true;
 	}
-	
-	public boolean canDisplayPredicate(String predicateUri, RoleLevel userRole) {
-	    return canDisplayPredicate(predicateUri, null, userRole);
-	}
 
 	/**
 	 * If display of a predicate is restricted, the user's role must be at least
 	 * as high as the restriction level.
 	 */
-	public boolean canDisplayPredicate(String predicateUri, String rangeUri, RoleLevel userRole) {
+	public boolean canDisplayPredicate(Property predicate, RoleLevel userRole) {	    
-		if (predicateUri == null) {
+		if (predicate == null) {
-			log.debug("can't display predicate: predicateUri was null");
+			log.debug("can't display predicate: predicate was null");
 			return false;
 		}
 		
-		RoleLevel displayThreshold = RoleLevel.NOBODY;
+		RoleLevel displayThreshold = getThreshold(predicate, displayThresholdMap);		
-		if (rangeUri == null) {
-		    displayThreshold = displayThresholdMap.get(predicateUri); 
-		} else {
-		    log.debug("Getting display threshold for " + predicateUri + " " + rangeUri);
-		    displayThreshold = getDisplayThreshold(predicateUri, rangeUri);
-		    if (displayThreshold == null) {
-		        displayThreshold = displayThresholdMap.get(predicateUri);
-		    }
-		    log.debug(displayThreshold);
-		}
 		       	        
 		if (isAuthorized(userRole, displayThreshold)) {
-			log.debug("can display predicate: '" + predicateUri
+            log.debug("can display predicate: '" + predicate.getURI() + "', domain=" 
-					+ "', userRole=" + userRole + ", thresholdRole="
+                    + predicate.getDomainVClassURI() + ", range=" 
-					+ displayThreshold);
+                    + predicate.getRangeVClassURI() + ", userRole="
+                    + userRole + ", thresholdRole=" + displayThreshold);
 			return true;
 		}
 
-		log.debug("can't display predicate: '" + predicateUri + "', userRole="
+        log.debug("can't display predicate: '" + predicate.getURI() + "', domain=" 
-				+ userRole + ", thresholdRole=" + displayThreshold);
+                + predicate.getDomainVClassURI() + ", range=" 
+                + predicate.getRangeVClassURI() + ", userRole="
+                + userRole + ", thresholdRole=" + displayThreshold);
 		return false;
 	}
 	
-	/**
-	 * Gets the role level threshold for displaying a predicate with a particular
-	 * object class
-	 * @param predicateUri
-	 * @param rangeUri
-	 * @return RoleLevel threshold
-	 */
-	private RoleLevel getDisplayThreshold(String predicateUri, String rangeUri) {
-	    String query = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
-                "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
-	            "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
-                "SELECT ?level WHERE { \n" +
-//                "    ?p rdfs:subPropertyOf ?property . \n" +
-                "    ?context config:configContextFor ?p . \n" +
-                "    ?context config:qualifiedBy ?range . \n" +
-                "    ?context config:hasConfiguration ?configuration . \n" +
-                "    ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?level \n" +
-                "}";
-	    Query q = QueryFactory.create(query);
-	    QueryExecution qe = QueryExecutionFactory.create(q, displayModel);
-	    try {
-	        ResultSet rs = qe.execSelect();
-	        if (!rs.hasNext()) {
-	            return null;
-	        } 
-	        while(rs.hasNext()) {
-	          QuerySolution qsoln = rs.nextSolution();
-	          Resource levelRes = qsoln.getResource("level");
-	          if (levelRes != null) {
-	              return RoleLevel.getRoleByUri(levelRes.getURI());
-	          }
-	        }
-	    } finally {
-	        qe.close();
-	    }
-	    return null;
-	}
-	
 	/**
 	 * A predicate cannot be modified if its namespace is in the prohibited list
 	 * (some exceptions are allowed).
@@ -355,32 +375,36 @@ public class PropertyRestrictionPolicyHelper {
 	 * If modification of a predicate is restricted, the user's role must be at
 	 * least as high as the restriction level.
 	 */
-	public boolean canModifyPredicate(String predicateUri, RoleLevel userRole) {
+	public boolean canModifyPredicate(Property predicate, RoleLevel userRole) {
-		if (predicateUri == null) {
+		if (predicate == null || predicate.getURI() == null) {
-			log.debug("can't modify predicate: predicateUri was null");
+			log.debug("can't modify predicate: predicate was null");
 			return false;
 		}
 
-		if (modifyProhibitedNamespaces.contains(namespace(predicateUri))) {
+		if (modifyProhibitedNamespaces.contains(namespace(predicate.getURI()))) {
-			if (modifyExceptionsAllowedUris.contains(predicateUri)) {
+			if (modifyExceptionsAllowedUris.contains(predicate.getURI())) {
-				log.debug("'" + predicateUri + "' is a permitted exception");
+				log.debug("'" + predicate.getURI() + "' is a permitted exception");
 			} else {
-				log.debug("can't modify resource '" + predicateUri
+				log.debug("can't modify resource '" + predicate.getURI()
 						+ "': prohibited namespace: '"
-						+ namespace(predicateUri) + "'");
+						+ namespace(predicate.getURI()) + "'");
 				return false;
 			}
 		}
 
-		RoleLevel modifyThreshold = modifyThresholdMap.get(predicateUri);
+		RoleLevel modifyThreshold = getModifyThreshold(predicate);
 		if (isAuthorized(userRole, modifyThreshold)) {
-			log.debug("can modify predicate: '" + predicateUri + "', userRole="
+			log.debug("can modify predicate: '" + predicate.getURI() + "', domain=" 
+		            + predicate.getDomainVClassURI() + ", range=" 
+			        + predicate.getRangeVClassURI() + ", userRole="
 					+ userRole + ", thresholdRole=" + modifyThreshold);
 			return true;
 		}
 
-		log.debug("can't modify predicate: '" + predicateUri + "', userRole="
+        log.debug("can't modify predicate: '" + predicate.getURI() + "', domain=" 
-				+ userRole + ", thresholdRole=" + modifyThreshold);
+                + predicate.getDomainVClassURI() + ", range=" 
+                + predicate.getRangeVClassURI() + ", userRole="
+                + userRole + ", thresholdRole=" + modifyThreshold);
 		return false;
 	}
 
@@ -422,7 +446,7 @@ public class PropertyRestrictionPolicyHelper {
                     throw new NullPointerException(
                             "display model has not been initialized.");
                 }
-				
+                
 				PropertyRestrictionPolicyHelper bean = PropertyRestrictionPolicyHelper
 						.createBean(model, displayModel);
 				PropertyRestrictionPolicyHelper.setBean(ctx, bean);

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/specialrelationships/AbstractRelationshipPolicy.java

@@ -13,6 +13,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.Authorization;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.PolicyDecision;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.PolicyIface;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A collection of building-block methods so we can code a policy based on the
@@ -34,9 +35,9 @@ public abstract class AbstractRelationshipPolicy implements PolicyIface {
 				uri, RoleLevel.SELF);
 	}
 
-	protected boolean canModifyPredicate(String uri) {
+	protected boolean canModifyPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx).canModifyPredicate(
-				uri, RoleLevel.SELF);
+				predicate, RoleLevel.SELF);
 	}
 
 	protected PolicyDecision cantModifyResource(String uri) {

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/ifaces/RequestActionConstants.java

@@ -2,9 +2,12 @@
 
 package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces;
 
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
+
 public class RequestActionConstants {
     public static String actionNamespace = "java:";
     
     public static String SOME_URI = "?SOME_URI";
+    public static Property SOME_PREDICATE = new Property(SOME_URI);
     public static String SOME_LITERAL = "?SOME_LITERAL";
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/AbstractDataPropertyStatementAction.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A base class for requested actions that involve adding, editing, or dropping
@@ -14,12 +15,16 @@ public abstract class AbstractDataPropertyStatementAction extends
 		AbstractPropertyStatementAction {
 	private final String subjectUri;
 	private final String predicateUri;
+	private final Property predicate;
 
 	public AbstractDataPropertyStatementAction(OntModel ontModel,
 			String subjectUri, String predicateUri) {
 		super(ontModel);
 		this.subjectUri = subjectUri;
 		this.predicateUri = predicateUri;
+		Property dataProperty = new Property();
+		dataProperty.setURI(predicateUri);
+		this.predicate = dataProperty;
 	}
 
 	public AbstractDataPropertyStatementAction(OntModel ontModel,
@@ -28,12 +33,19 @@ public abstract class AbstractDataPropertyStatementAction extends
 		this.subjectUri = (dps.getIndividual() == null) ? dps
 				.getIndividualURI() : dps.getIndividual().getURI();
 		this.predicateUri = dps.getDatapropURI();
+	    Property dataProperty = new Property();
+	    dataProperty.setURI(predicateUri);
+	    this.predicate = dataProperty;
 	}
 
 	public String getSubjectUri() {
 		return subjectUri;
 	}
 
+	public Property getPredicate() {
+	    return predicate;
+	}
+	
 	@Override
 	public String getPredicateUri() {
 		return predicateUri;

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/AbstractObjectPropertyStatementAction.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A base class for requested actions that involve adding, editing, or deleting
@@ -13,14 +14,14 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 public abstract class AbstractObjectPropertyStatementAction extends
 		AbstractPropertyStatementAction {
 	private final String subjectUri;
-	private final String predicateUri;
+	private final Property predicate;
 	private final String objectUri;
 
 	public AbstractObjectPropertyStatementAction(OntModel ontModel, String subjectUri,
-			String predicateUri, String objectUri) {
+			Property predicate, String objectUri) {
 		super(ontModel);
 		this.subjectUri = subjectUri;
-		this.predicateUri = predicateUri;
+		this.predicate = predicate;
 		this.objectUri = objectUri;
 	}
 
@@ -28,8 +29,7 @@ public abstract class AbstractObjectPropertyStatementAction extends
 		super(ontModel);
 		this.subjectUri = (ops.getSubject() == null) ? ops.getSubjectURI()
 				: ops.getSubject().getURI();
-		this.predicateUri = (ops.getProperty() == null) ? ops.getPropertyURI()
+		this.predicate = (ops.getProperty());
-				: ops.getProperty().getURI();
 		this.objectUri = (ops.getObject() == null) ? ops.getObjectURI() : ops
 				.getObject().getURI();
 	}
@@ -42,9 +42,13 @@ public abstract class AbstractObjectPropertyStatementAction extends
 		return objectUri;
 	}
 	
+	public Property getPredicate() {
+	    return predicate;
+	}
+	
 	@Override
 	public String getPredicateUri() {
-		return predicateUri;
+		return predicate.getURI();
 	}
 
 	@Override
@@ -55,6 +59,6 @@ public abstract class AbstractObjectPropertyStatementAction extends
 	@Override
 	public String toString() {
 		return this.getClass().getSimpleName() + ": <" + subjectUri + "> <"
-				+ predicateUri + "> <" + objectUri + ">";
+				+ predicate.getURI() + "> <" + objectUri + ">";
 	}
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/AbstractPropertyStatementAction.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAction;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A base class for requested actions that involve adding, editing, or deleting
@@ -27,5 +28,7 @@ public abstract class AbstractPropertyStatementAction extends RequestedAction {
 	 */
 	public abstract String[] getResourceUris();
 
+	public abstract Property getPredicate();
+	
 	public abstract String getPredicateUri();
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/AddObjectPropertyStatement.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Should we allow the user to add this ObjectPropertyStatement to this model?
@@ -12,8 +13,8 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 public class AddObjectPropertyStatement extends
 		AbstractObjectPropertyStatementAction {
 	public AddObjectPropertyStatement(OntModel ontModel, String uriOfSub,
-			String uriOfPred, String uriOfObj) {
+			Property predicate, String uriOfObj) {
-		super(ontModel, uriOfSub, uriOfPred, uriOfObj);
+		super(ontModel, uriOfSub, predicate, uriOfObj);
 	}
 
 	public AddObjectPropertyStatement(OntModel ontModel,

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/DropObjectPropertyStatement.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Should we allow the user to delete this ObjectPropertyStatement from this
@@ -13,7 +14,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 public class DropObjectPropertyStatement extends
 		AbstractObjectPropertyStatementAction {
 	public DropObjectPropertyStatement(OntModel ontModel, String sub,
-			String pred, String obj) {
+			Property pred, String obj) {
 		super(ontModel, sub, pred, obj);
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/EditObjectPropertyStatement.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Should we allow the user to edit this ObjectPropertyStatement in this model?
@@ -12,8 +13,8 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 public class EditObjectPropertyStatement extends
 		AbstractObjectPropertyStatementAction {
 	public EditObjectPropertyStatement(OntModel ontModel, String subjectUri,
-			String keywordPredUri, String objectUri) {
+			Property keywordPred, String objectUri) {
-		super(ontModel, subjectUri, keywordPredUri, objectUri);
+		super(ontModel, subjectUri, keywordPred, objectUri);
 	}
 
 	public EditObjectPropertyStatement(OntModel ontModel,

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

@@ -78,10 +78,12 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
         e.writeObject(this);
     }
 
-
+    @Override
     public String getDomainVClassURI() {
         return domainVClassURI;
     }
+    
+    @Override
     public void setDomainVClassURI(String domainClassURI) {
         this.domainVClassURI = domainClassURI;
     }
@@ -111,9 +113,13 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
     public void setParentURI(String parentURI) {
         this.parentURI = parentURI;
     }
+    
+    @Override
     public String getRangeVClassURI() {
         return rangeVClassURI;
     }
+    
+    @Override
     public void setRangeVClassURI(String rangeClassURI) {
         this.rangeVClassURI = rangeClassURI;
     }

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

@@ -15,11 +15,20 @@ public class Property extends BaseResourceBean {
     private String  groupURI              = null;
     private String  label                 = null; // keep so can set in a context-specific way
     private final boolean subjectSide     = true; // only relevant to ObjectProperty
+    private String domainVClassURI        = null;
+    private String rangeVClassURI         = null;
+    private boolean editLinkSuppressed    = false;
+    private boolean addLinkSuppressed     = false;
+    private boolean deleteLinkSuppressed  = false;
     
     public Property() {
         this.groupURI = null;
         this.label = null;
     }
+    
+    public Property(String URI) {
+        this.setURI(URI);
+    }
 
     public String getCustomEntryForm() {
         return customEntryForm;
@@ -43,10 +52,53 @@ public class Property extends BaseResourceBean {
         this.label = label;
     }
     
+    public String getDomainVClassURI() {
+        return this.domainVClassURI;
+    }
+    
+    public void setDomainVClassURI(String domainVClassURI) {
+        this.domainVClassURI = domainVClassURI;
+    }
+    
+    public String getRangeVClassURI() {
+        return this.rangeVClassURI;
+    }
+    
+    public void setRangeVClassURI(String rangeVClassURI) {
+        this.rangeVClassURI = rangeVClassURI;
+    }
+    
     public boolean isSubjectSide() {
         return subjectSide;
     }
     
+    public boolean isEditLinkSuppressed() {
+        return editLinkSuppressed;
+    }
+    
+    public boolean isAddLinkSuppressed() {
+        return addLinkSuppressed;
+    }
+    
+    public boolean isDeleteLinkSuppressed() {
+        return deleteLinkSuppressed;
+    }
+    
+    public void setEditLinkSuppressed(boolean editLinkSuppressed) {
+        this.editLinkSuppressed = editLinkSuppressed;
+    }
+    
+    public void setAddLinkSuppressed(boolean addLinkSuppressed) {
+        if (this.addLinkSuppressed) {
+            throw new RuntimeException("addLinkSuppressed already true");
+        }
+        this.addLinkSuppressed = addLinkSuppressed;
+    }
+    
+    public void setDeleteLinkSuppressed(boolean deleteLinkSuppressed) {
+        this.deleteLinkSuppressed = deleteLinkSuppressed;
+    }
+    
     /**
      * Sorts Property objects, by property rank, then alphanumeric.
      * @author bdc34

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

@@ -3,6 +3,8 @@
 package edu.cornell.mannlib.vitro.webapp.beans;
 
 import java.text.Collator;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.openrdf.model.impl.URIImpl;
 
@@ -91,6 +93,9 @@ public class VClass extends BaseResourceBean implements Comparable<VClass>
     public Float getSearchBoost() { return searchBoost; }
     public void setSearchBoost( Float boost ){ searchBoost = boost;}
     
+    public boolean isUnion() { return false; }
+    public List<VClass> getUnionComponents() { return new ArrayList<VClass>(); }
+    
     /**
      * Default constructor
      */

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

@@ -9,9 +9,11 @@ import java.io.PrintWriter;
 import java.io.Writer;
 import java.net.URLDecoder;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 import javax.servlet.RequestDispatcher;
 import javax.servlet.ServletException;
@@ -40,6 +42,7 @@ import com.hp.hpl.jena.vocabulary.XSD;
 import edu.cornell.mannlib.vedit.controller.BaseEditController;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
+import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualController;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
@@ -47,45 +50,37 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ResultFormat;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.web.ContentType;
 
 
 /**
- * Services a sparql query.  This will return a simple error message and a 501 if
+ * Services a SPARQL query.  This will return a simple error message and a 501 if
  * there is no Model.
  *
+ *
  * @author bdc34
  *
  */
 public class SparqlQueryServlet extends BaseEditController {
     private static final Log log = LogFactory.getLog(SparqlQueryServlet.class.getName());
-
-    private final static boolean CONVERT = true;
     
     /**
      * format configurations for SELECT queries.
      */
     protected static HashMap<String,RSFormatConfig> rsFormats = new HashMap<String,RSFormatConfig>();
-
+   
-    private static RSFormatConfig[] rsfs = {
-        new RSFormatConfig( "RS_XML", !CONVERT, ResultFormat.XML, null, "text/xml"),
-        new RSFormatConfig( "RS_TEXT", !CONVERT, ResultFormat.TEXT, null, "text/plain"),
-        new RSFormatConfig( "vitro:csv", !CONVERT, ResultFormat.CSV, null, "text/csv"),
-        new RSFormatConfig( "RS_JSON", !CONVERT, ResultFormat.JSON, null, "application/javascript") };        
-    
     /**
      * format configurations for CONSTRUCT/DESCRIBE queries.
      */
     protected static HashMap<String,ModelFormatConfig> modelFormats = 
         new HashMap<String,ModelFormatConfig>();
 
-    private static ModelFormatConfig[] fmts = {
+    /**
-        new ModelFormatConfig("RDF/XML", !CONVERT, ModelSerializationFormat.RDFXML, null, "application/rdf+xml" ),
+     * Use this map to decide which MIME type is suited for the "accept" header.
-        new ModelFormatConfig("RDF/XML-ABBREV", CONVERT, ModelSerializationFormat.N3, "RDF/XML-ABBREV", "application/rdf+xml" ),
+     */
-        new ModelFormatConfig("N3", !CONVERT, ModelSerializationFormat.N3, null, "text/n3" ),
+    public static final Map<String, Float> ACCEPTED_CONTENT_TYPES;
-        new ModelFormatConfig("N-TRIPLE", !CONVERT, ModelSerializationFormat.NTRIPLE, null, "text/plain" ),
-        new ModelFormatConfig("TTL", CONVERT, ModelSerializationFormat.N3, "TTL", "application/x-turtle" ),
-        new ModelFormatConfig("JSON-LD", CONVERT, ModelSerializationFormat.N3, "JSON-LD", "application/javascript" ) };
 
+   
     @Override
     protected void doPost(HttpServletRequest request, HttpServletResponse response)
     throws ServletException, IOException
@@ -113,100 +108,85 @@ public class SparqlQueryServlet extends BaseEditController {
         String queryParam = vreq.getParameter("query");
         log.debug("queryParam was : " + queryParam);
 
-        String resultFormatParam = vreq.getParameter("resultFormat");
+        if( queryParam == null || "".equals(queryParam) ){
-        log.debug("resultFormat was: " + resultFormatParam);
-        
-        String rdfResultFormatParam = vreq.getParameter("rdfResultFormat");
-        if (rdfResultFormatParam == null) {
-        	rdfResultFormatParam = "RDF/XML-ABBREV";
-        }
-        log.debug("rdfResultFormat was: " + rdfResultFormatParam);
-
-        if( queryParam == null || "".equals(queryParam) ||
-            resultFormatParam == null || "".equals(resultFormatParam) ||
-            !rsFormats.containsKey( resultFormatParam ) || 
-            rdfResultFormatParam == null || "".equals(rdfResultFormatParam) ||
-            !modelFormats.containsKey( rdfResultFormatParam ) ) {
             doHelp(request,response);
             return;
         }
-
+        
-        executeQuery(response, resultFormatParam, rdfResultFormatParam, 
+        String contentType = checkForContentType(vreq.getHeader("Accept"));        
-                queryParam, vreq.getUnfilteredRDFService()); 
+        
+        Query query = SparqlQueryUtils.create(queryParam);
+        if( query.isSelectType() ){            
+            String format =  contentType!=null ? contentType:vreq.getParameter("resultFormat");            
+            RSFormatConfig formatConf = rsFormats.get(format);                    
+            doSelect(response, queryParam, formatConf, vreq.getRDFService());            
+        }else if( query.isAskType()){
+            doAsk( queryParam, vreq.getRDFService(), response ); 
+        }else if( query.isConstructType() ){
+            String format = contentType != null ? contentType : vreq.getParameter("rdfResultFormat");                        
+            if (format== null) {
+                format= "RDF/XML-ABBREV";
+            }            
+            ModelFormatConfig formatConf = modelFormats.get(format);
+            doConstruct(response, query, formatConf, vreq.getRDFService());
+        }else{
+            doHelp(request,response);            
+        }
         return;
     }
     
-    private void executeQuery(HttpServletResponse response, 
-                              String resultFormatParam, 
-                              String rdfResultFormatParam, 
-                              String queryParam, 
-                              RDFService rdfService ) throws IOException {        
-    	/* BJL23 2008-11-06
-    	 * modified to support CSV output.
-    	 * Unfortunately, ARQ doesn't make it easy to
-    	 * do this by implementing a new ResultSetFormat, because 
-    	 * ResultSetFormatter is hardwired with expected values.
-    	 * This slightly ugly approach will have to do for now.
-    	 */            	
-//        if ( !("vitro:csv").equals(resultFormatParam) ) {
-//        	rsf = selectFormatSymbols.get(resultFormatParam);
-//        }                       
-//        String mimeType = rdfFormatToMimeType.get(resultFormatParam);
-        
-        try{
-            Query query = SparqlQueryUtils.create(queryParam);
-            if( query.isSelectType() ){
-                doSelectQuery( queryParam, rdfService, resultFormatParam, response);
-            } else if(query.isAskType()){
-                // Irrespective of the ResultFormatParam, 
-                // this always prints a boolean to the default OutputStream.
-                String result = (rdfService.sparqlAskQuery(queryParam) == true) 
-                    ? "true" 
-                    : "false";
-                PrintWriter p = response.getWriter();
-                p.write(result);
-                return;                
-            } else {                
-                doModelResultQuery( query, rdfService, rdfResultFormatParam, response);
-            }
-        } catch (RDFServiceException e) {
-                throw new RuntimeException(e);
-        }
-    }
 
+    private void doAsk(String queryParam, RDFService rdfService,
+            HttpServletResponse response) throws ServletException, IOException {
+        
+        // Irrespective of the ResultFormatParam, 
+        // this always prints a boolean to the default OutputStream.
+        String result;
+        try {
+            result = (rdfService.sparqlAskQuery(queryParam) == true) 
+                ? "true" 
+                : "false";
+        } catch (RDFServiceException e) {
+            throw new ServletException( "Could not execute ask query ", e );
+        }
+        PrintWriter p = response.getWriter();
+        p.write(result);
+        return;
+    }
+    
     /**
      * Execute the query and send the result to out. Attempt to
      * send the RDFService the same format as the rdfResultFormatParam
      * so that the results from the RDFService can be directly piped to the client.
-     * @param rdfService 
-     * @throws IOException 
-     * @throws RDFServiceException 
      */
-    private void doSelectQuery( String queryParam,
+    private void doSelect(HttpServletResponse response,
-                                RDFService rdfService, String resultFormatParam,
+                                String queryParam,
-                                HttpServletResponse response) throws IOException, RDFServiceException{                
+                                RSFormatConfig formatConf, 
-        RSFormatConfig config = rsFormats.get( resultFormatParam );
+                                RDFService rdfService 
+                                ) throws ServletException {
+        try {
+            if( ! formatConf.converstionFromWireFormat ){
+                response.setContentType( formatConf.responseMimeType );
+                InputStream results;                
+                results = rdfService.sparqlSelectQuery(queryParam, formatConf.wireFormat );
+                pipe( results, response.getOutputStream() );
+            }else{                        
+                //always use JSON when conversion is needed.
+                InputStream results = rdfService.sparqlSelectQuery(queryParam, ResultFormat.JSON );
                 
-        if( ! config.converstionFromWireFormat ){
+                response.setContentType( formatConf.responseMimeType );
-            response.setContentType( config.responseMimeType );
+                            
-            InputStream results = rdfService.sparqlSelectQuery(queryParam, config.wireFormat );                        
+                ResultSet rs = ResultSetFactory.fromJSON( results );            
-            pipe( results, response.getOutputStream() );
+                OutputStream out = response.getOutputStream();
-        }else{                        
+                ResultSetFormatter.output(out, rs, formatConf.jenaResponseFormat);                
-            //always use JSON when conversion is needed.
+            }
-            InputStream results = rdfService.sparqlSelectQuery(queryParam, ResultFormat.JSON );
+        } catch (RDFServiceException e) {
-            
+            throw new ServletException("Cannot get result from the RDFService",e);
-            response.setContentType( config.responseMimeType );
+        } catch (IOException e) {
-                        
+            throw new ServletException("Cannot perform SPARQL SELECT",e);
-            ResultSet rs = ResultSetFactory.fromJSON( results );            
-            OutputStream out = response.getOutputStream();
-            ResultSetFormatter.output(out, rs, config.jenaResponseFormat);
-            
-            // } else {
-            //     Writer out = response.getWriter();
-            //     toCsv(out, results);
-            //}
         }
     }
+    
 
     /**
      * Execute the query and send the result to out. Attempt to
@@ -217,40 +197,44 @@ public class SparqlQueryServlet extends BaseEditController {
      * @throws RDFServiceException 
      * @throws  
      */
-    private void doModelResultQuery( Query query, 
+    private void doConstruct( HttpServletResponse response, 
-                                      RDFService rdfService, String rdfResultFormatParam, 
+                               Query query, 
-                                      HttpServletResponse response) throws IOException, RDFServiceException{
+                               ModelFormatConfig formatConfig,
-
+                               RDFService rdfService 
-        //config drives what formats and conversions to use 
+                               ) throws ServletException{
-        ModelFormatConfig config = modelFormats.get( rdfResultFormatParam );
+        try{
-
+            InputStream rawResult = null;        
-        InputStream rawResult = null;        
+            if( query.isConstructType() ){                    
-        if( query.isConstructType() ){                    
+                rawResult= rdfService.sparqlConstructQuery( query.toString(), formatConfig.wireFormat );
-            rawResult= rdfService.sparqlConstructQuery( query.toString(), config.wireFormat );
+            }else if ( query.isDescribeType() ){
-        }else if ( query.isDescribeType() ){
+                rawResult = rdfService.sparqlDescribeQuery( query.toString(), formatConfig.wireFormat );
-            rawResult = rdfService.sparqlDescribeQuery( query.toString(), config.wireFormat );
+            }
-        }
+    
-
+            response.setContentType(  formatConfig.responseMimeType );
-        response.setContentType(  config.responseMimeType );
+            
-        
+            if( formatConfig.converstionFromWireFormat ){
-        if( config.converstionFromWireFormat ){
+                Model resultModel = RDFServiceUtils.parseModel( rawResult, formatConfig.wireFormat );                        
-            Model resultModel = RDFServiceUtils.parseModel( rawResult, config.wireFormat );                        
+                if( "JSON-LD".equals( formatConfig.jenaResponseFormat )){
-            if( "JSON-LD".equals( config.jenaResponseFormat )){
+                    //since jena 2.6.4 doesn't support JSON-LD we do it                                                                   
-                //since jena 2.6.4 doesn't support JSON-LD we do it                                                                   
+                    try {
-                try {
+                        JenaRDFParser parser = new JenaRDFParser();
-                    JenaRDFParser parser = new JenaRDFParser();
+                        Object json = JSONLD.fromRDF(resultModel, parser);
-                    Object json = JSONLD.fromRDF(resultModel, parser);
+                        JSONUtils.write(response.getWriter(), json);
-                    JSONUtils.write(response.getWriter(), json);
+                    } catch (JSONLDProcessingError e) {
-                } catch (JSONLDProcessingError e) {
+                       throw new RDFServiceException("Could not convert from Jena model to JSON-LD", e);
-                   throw new RDFServiceException("Could not convert from Jena model to JSON-LD", e);
+                    }
+                }else{
+                    OutputStream out = response.getOutputStream();
+                    resultModel.write(out, formatConfig.jenaResponseFormat );
                 }
             }else{
                 OutputStream out = response.getOutputStream();
-                resultModel.write(out, config.jenaResponseFormat );
+                pipe( rawResult, out );
             }
-        }else{
+        }catch( IOException ex){
-            OutputStream out = response.getOutputStream();
+            throw new ServletException("could not run SPARQL CONSTRUCT",ex);
-            pipe( rawResult, out );
+        } catch (RDFServiceException ex) {
+            throw new ServletException("could not run SPARQL CONSTRUCT",ex);
         }
     }
 
@@ -362,13 +346,35 @@ public class SparqlQueryServlet extends BaseEditController {
             rd.forward(req,res);
     }
 
+    /** Simple boolean vaule to improve the legibility of confiugrations. */
+    private final static boolean CONVERT = true;
 
-    public static class ModelFormatConfig{
+    /** Simple vaule to improve the legibility of confiugrations. */
+    private final static String NO_CONVERSION = null;
+
+    public static class FormatConfig{
         public String valueFromForm;
         public boolean converstionFromWireFormat;
-        public RDFService.ModelSerializationFormat wireFormat;
-        public String jenaResponseFormat;
         public String responseMimeType;
+    }
+    
+    private static ModelFormatConfig[] fmts = {
+        new ModelFormatConfig("RDF/XML", 
+                              !CONVERT, ModelSerializationFormat.RDFXML,  NO_CONVERSION,    "application/rdf+xml" ),
+        new ModelFormatConfig("RDF/XML-ABBREV", 
+                              CONVERT,  ModelSerializationFormat.N3,      "RDF/XML-ABBREV", "application/rdf+xml" ),
+        new ModelFormatConfig("N3", 
+                              !CONVERT, ModelSerializationFormat.N3,      NO_CONVERSION,    "text/n3" ),
+        new ModelFormatConfig("N-TRIPLE", 
+                              !CONVERT, ModelSerializationFormat.NTRIPLE, NO_CONVERSION,    "text/plain" ),
+        new ModelFormatConfig("TTL", 
+                              CONVERT,  ModelSerializationFormat.N3,      "TTL",            "application/x-turtle" ),
+        new ModelFormatConfig("JSON-LD", 
+                              CONVERT,  ModelSerializationFormat.N3,      "JSON-LD",        "application/javascript" ) };
+
+    public static class ModelFormatConfig extends FormatConfig{                
+        public RDFService.ModelSerializationFormat wireFormat;
+        public String jenaResponseFormat;        
         
         public ModelFormatConfig( String valueFromForm,
                                   boolean converstionFromWireFormat, 
@@ -383,12 +389,20 @@ public class SparqlQueryServlet extends BaseEditController {
         }
     }
 
-    public static class RSFormatConfig{
+
-        public String valueFromForm;
+    private static RSFormatConfig[] rsfs = {
-        public boolean converstionFromWireFormat;
+        new RSFormatConfig( "RS_XML", 
+                            !CONVERT, ResultFormat.XML,  null, "text/xml"),
+        new RSFormatConfig( "RS_TEXT", 
+                            !CONVERT, ResultFormat.TEXT, null, "text/plain"),
+        new RSFormatConfig( "vitro:csv", 
+                            !CONVERT, ResultFormat.CSV,  null, "text/csv"),
+        new RSFormatConfig( "RS_JSON", 
+                            !CONVERT, ResultFormat.JSON, null, "application/javascript") }; 
+
+    public static class RSFormatConfig extends FormatConfig{        
         public ResultFormat wireFormat;
         public ResultSetFormat jenaResponseFormat;
-        public String responseMimeType;
         
         public RSFormatConfig( String valueFromForm,
                                boolean converstionFromWireFormat,
@@ -403,14 +417,48 @@ public class SparqlQueryServlet extends BaseEditController {
         }    
     }
 
-    static{                
+    static{
-        /* move the lists of configs into maps for easy lookup */
+        HashMap<String, Float> map = new HashMap<String, Float>();
+        
+        /* move the lists of configurations into maps for easy lookup
+         * by both MIME content type and the parameters from the form */
         for( RSFormatConfig rsfc : rsfs ){
             rsFormats.put( rsfc.valueFromForm, rsfc );
+            rsFormats.put( rsfc.responseMimeType, rsfc);
+            map.put(rsfc.responseMimeType, 1.0f);
         }
         for( ModelFormatConfig mfc : fmts ){
             modelFormats.put( mfc.valueFromForm, mfc);
-        }        
+            modelFormats.put(mfc.responseMimeType, mfc);
+            map.put(mfc.responseMimeType, 1.0f);
+        }
+        
+        ACCEPTED_CONTENT_TYPES = Collections.unmodifiableMap(map);
     }
 
+
+    /**
+     * Get the content type based on content negotiation.
+     * Returns null of no content type can be agreed on or
+     * if there is no accept header.   
+     */
+    protected String checkForContentType( String acceptHeader ) {        
+        if (acceptHeader == null) 
+            return null;        
+    
+        try {
+            Map<String, Float> typesAndQ = ContentType
+                    .getTypesAndQ(acceptHeader);
+            
+            String ctStr = ContentType
+                    .getBestContentType(typesAndQ,ACCEPTED_CONTENT_TYPES); 
+                    
+            if( ACCEPTED_CONTENT_TYPES.containsKey( ctStr )){
+                return ctStr;
+            }
+        } catch (Throwable th) {
+            log.error("Problem while checking accept header ", th);
+        }
+        return null;
+    }
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/admin/ShowAuthController.java

@@ -91,7 +91,7 @@ public class ShowAuthController extends FreemarkerHttpServlet {
 	private boolean mayEditIndividual(VitroRequest vreq, String individualUri) {
 		RequestedAction action = new EditObjectPropertyStatement(
 				vreq.getJenaOntModel(), individualUri,
-				RequestActionConstants.SOME_URI,
+				RequestActionConstants.SOME_PREDICATE,
 				RequestActionConstants.SOME_URI);
 		return PolicyHelper.isAuthorizedForActions(vreq, action);
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Classes2ClassesRetryController.java

@@ -19,6 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
 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.VClassDao;
 
 public class Classes2ClassesRetryController extends BaseEditController {
@@ -43,7 +44,7 @@ public class Classes2ClassesRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        VClassDao vcDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = ModelAccess.on(getServletContext()).getWebappDaoFactory().getVClassDao();
         epo.setDataAccessObject(vcDao);
         Classes2Classes objectForEditing = new Classes2Classes();
 

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

@@ -22,6 +22,7 @@ import edu.cornell.mannlib.vedit.forwarder.impl.UrlForwarder;
 import edu.cornell.mannlib.vedit.util.FormUtils;
 import edu.cornell.mannlib.vedit.validator.Validator;
 import edu.cornell.mannlib.vedit.validator.impl.RequiredFieldValidator;
+import edu.cornell.mannlib.vedit.validator.impl.UrlValidator;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
@@ -47,7 +48,13 @@ public class OntologyRetryController extends BaseEditController {
         epo.setBeanClass(Ontology.class);
         epo.setBeanMask(testMask);
 
-        String action = "insert";
+        String action = null;
+        if (epo.getAction() == null) {
+            action = "insert";
+            epo.setAction("insert");
+        } else {
+            action = epo.getAction();
+        }
 
         OntologyDao oDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
         epo.setDataAccessObject(oDao);
@@ -67,13 +74,12 @@ public class OntologyRetryController extends BaseEditController {
             epo.setOriginalBean(ontologyForEditing);
         } else {
             ontologyForEditing = (Ontology) epo.getNewBean();
-            action = "update";
-            log.error("using newBean");
         }
         
         //validators
         List<Validator> validatorList = new ArrayList<Validator>();
         validatorList.add(new RequiredFieldValidator());
+        validatorList.add(new UrlValidator());
         epo.getValidatorMap().put("URI", validatorList);
 
         //make a simple mask for the class's id

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

@@ -37,6 +37,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.edit.utils.RoleLevelOptionsSetup;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
@@ -69,7 +70,8 @@ public class PropertyRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        ObjectPropertyDao propDao = request.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao propDao = ModelAccess.on(getServletContext()).getWebappDaoFactory().getObjectPropertyDao();
+                //getUnfilteredWebappDaoFactory().getObjectPropertyDao();
         epo.setDataAccessObject(propDao);
         OntologyDao ontDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
         VClassDao vclassDao = request.getUnfilteredWebappDaoFactory().getVClassDao();

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

@@ -24,6 +24,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
 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.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
@@ -44,7 +45,7 @@ public class VclassEditController extends BaseEditController {
         EditProcessObject epo = super.createEpo(request, FORCE_NEW);
         request.setAttribute("epoKey", epo.getKey());
 
-        VClassDao vcwDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
+        VClassDao vcwDao = ModelAccess.on(getServletContext()).getBaseWebappDaoFactory().getVClassDao();
         VClass vcl = (VClass)vcwDao.getVClassByURI(request.getParameter("uri"));
         
         if (vcl == null) {
@@ -140,8 +141,8 @@ public class VclassEditController extends BaseEditController {
         HashMap formSelect = new HashMap(); // tells the JSP what select lists are populated, and thus should be displayed
         request.setAttribute("formSelect",formSelect);
 
-        // if supported, we want to show only the asserted superclasses and subclasses.  Don't want to see anonymous classes, restrictions, etc.
+        // if supported, we want to show only the asserted superclasses and subclasses.
-        VClassDao vcDao = request.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = ModelAccess.on(getServletContext()).getBaseWebappDaoFactory().getVClassDao();
         List superURIs = vcDao.getSuperClassURIs(vcl.getURI(),false);
         List superVClasses = new ArrayList();
         Iterator superURIit = superURIs.iterator();

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ImageUploadController.java

@@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AddObjectP
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.DropObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
@@ -146,20 +147,23 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 			String action = vreq.getParameter(PARAMETER_ACTION);
 			Individual entity = validateEntityUri(vreq);
 			String imageUri = entity.getMainImageUri();
+			
+			Property indMainImage = new Property();
+			indMainImage.setURI(VitroVocabulary.IND_MAIN_IMAGE);
 
 			RequestedAction ra;
 			if (ACTION_DELETE.equals(action)
 					|| ACTION_DELETE_EDIT.equals(action)) {
 				ra = new DropObjectPropertyStatement(vreq.getJenaOntModel(),
-						entity.getURI(), VitroVocabulary.IND_MAIN_IMAGE,
+						entity.getURI(), indMainImage,
 						imageUri);
 			} else if (imageUri != null) {
 				ra = new EditObjectPropertyStatement(vreq.getJenaOntModel(),
-						entity.getURI(), VitroVocabulary.IND_MAIN_IMAGE,
+						entity.getURI(), indMainImage,
 						imageUri);
 			} else {
 				ra = new AddObjectPropertyStatement(vreq.getJenaOntModel(),
-						entity.getURI(), VitroVocabulary.IND_MAIN_IMAGE,
+						entity.getURI(), indMainImage,
 						RequestActionConstants.SOME_URI);
 			}
 			return new Actions(ra);

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzer.java

@@ -132,10 +132,11 @@ public class IndividualRequestAnalyzer {
 	 * only provide a set of bytes.
 	 */
 	protected ContentType checkAcceptHeaderForLinkedDataRequest() {
-		String acceptHeader = vreq.getHeader("accept");
+		String acceptHeader = vreq.getHeader("Accept");
-		if (acceptHeader == null) {
+		if (acceptHeader == null) 
-			return null;
+		    acceptHeader = vreq.getHeader("accept");		   
-		}
+		if (acceptHeader == null)
+			return null;		
 	
 		try {
 			Map<String, Float> typesAndQ = ContentType

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

@@ -77,11 +77,16 @@ public class RDFUploadController extends JenaIngestController {
         VitroRequest request = new VitroRequest(req);        
         LoginStatusBean loginBean = LoginStatusBean.getBean(request);
         
-        String modelName = req.getParameter("modelName");
+        try {
-        if(modelName!=null){
+            String modelName = req.getParameter("modelName");
-            loadRDF(req,request,response);
+            if(modelName!=null){
-            return;
+                loadRDF(req,request,response);
-        }            
+                return;
+            }    
+        } catch (Exception e) {
+            log.error(e,e);
+            throw new RuntimeException(e);
+        }
                        
         boolean remove = "remove".equals(request.getParameter("mode"));
         String verb = remove?"Removed":"Added";

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

@@ -15,7 +15,7 @@ public interface ObjectPropertyDao extends PropertyDao {
 
     public ObjectProperty getObjectPropertyByURI(String objectPropertyURI);
     
-    public ObjectProperty getObjectPropertyByURIAndRangeURI(String objectPropertyURI, String rangeURI);
+    public ObjectProperty getObjectPropertyByURIs(String objectPropertyURI, String domainURI, String rangeURI);
 
     public List <ObjectProperty> getObjectPropertiesForObjectPropertyStatements(List /*of ObjectPropertyStatement */ objectPropertyStatements);
 

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

@@ -41,8 +41,8 @@ public interface ObjectPropertyStatementDao {
     public Map<String, String> getMostSpecificTypesInClassgroupsForIndividual(String subjectUri);
 
 	List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
-			String subjectUri, String propertyUri, String objectKey, String rangeUri,
+			String subjectUri, String propertyUri, String objectKey, String domainUri, 
-			String queryString, Set<String> constructQueryStrings,
+			String rangeUri, String queryString, Set<String> constructQueryStrings,
 			String sortDirection);
 
 	

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

@@ -7,10 +7,13 @@ public class VitroVocabulary {
 
 	
     public static final String vitroURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#";
+    public static final String configURI= "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#";
     
     public static final String VITRO_AUTH = "http://vitro.mannlib.cornell.edu/ns/vitro/authorization#";
     public static final String VITRO_PUBLIC = "http://vitro.mannlib.cornell.edu/ns/vitro/public#";
     public static final String VITRO_PUBLIC_ONTOLOGY = "http://vitro.mannlib.cornell.edu/ns/vitro/public";
+    // TODO change the following before 1.6 release
+    public static final String PROPERTY_CONFIG_DATA = "http://example.org/appConfig/";
     
     
     /** BJL23 2008-02-25:
@@ -95,6 +98,9 @@ public class VitroVocabulary {
     public static final String PROPERTY_CUSTOM_LIST_VIEW_ANNOT = vitroURI + "customListViewAnnot";
     public static final String PROPERTY_SELECTFROMEXISTINGANNOT = vitroURI+"selectFromExistingAnnot";
     public static final String PROPERTY_OFFERCREATENEWOPTIONANNOT = vitroURI+"offerCreateNewOptionAnnot";
+    public static final String PROPERTY_EDITLINKSUPPRESSED = configURI + "editLinkSuppressed";
+    public static final String PROPERTY_ADDLINKSUPPRESSED = configURI + "addLinkSuppressed";
+    public static final String PROPERTY_DELETELINKSUPPRESSED = configURI + "deleteLinkSuppressed";
     public static final String PROPERTY_INPROPERTYGROUPANNOT = vitroURI+"inPropertyGroupAnnot";
     public static final String PROPERTYGROUP = vitroURI + "PropertyGroup";
     public static final String MASKS_PROPERTY = vitroURI + "masksProperty";

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

@@ -49,8 +49,8 @@ class ObjectPropertyDaoFiltering extends BaseFiltering implements ObjectProperty
         return (newOprop == null) ? null : new ObjectPropertyFiltering(newOprop, filters);
     }
     
-    public ObjectProperty getObjectPropertyByURIAndRangeURI(String objectPropertyURI, String rangeURI) {
+    public ObjectProperty getObjectPropertyByURIs(String objectPropertyURI, String domainURI, String rangeURI) {
-        ObjectProperty newOprop=innerObjectPropertyDao.getObjectPropertyByURIAndRangeURI(objectPropertyURI, rangeURI);
+        ObjectProperty newOprop=innerObjectPropertyDao.getObjectPropertyByURIs(objectPropertyURI, domainURI, rangeURI);
         return (newOprop == null) ? null : new ObjectPropertyFiltering(newOprop, filters);
     }
 

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

@@ -523,6 +523,36 @@ public class ObjectPropertyFiltering extends ObjectProperty {
 	public void setCollateBySubclass(boolean collate) {		
 		innerObjectProperty.setCollateBySubclass(collate);
 	}
+	
+	@Override
+	public boolean isEditLinkSuppressed() {
+	    return innerObjectProperty.isEditLinkSuppressed();
+	}
+	
+	@Override 
+	public boolean isAddLinkSuppressed() {
+	    return innerObjectProperty.isAddLinkSuppressed();
+	}
+	
+	@Override 
+	public boolean isDeleteLinkSuppressed() {
+	    return innerObjectProperty.isDeleteLinkSuppressed();
+	}
+	
+	@Override
+    public void setEditLinkSuppressed(boolean editLinkSuppressed) {
+        innerObjectProperty.setEditLinkSuppressed(editLinkSuppressed);
+    }
+    
+    @Override 
+    public void setAddLinkSuppressed(boolean addLinkSuppressed) {
+        innerObjectProperty.setAddLinkSuppressed(addLinkSuppressed);
+    }
+    
+    @Override 
+    public void setDeleteLinkSuppressed(boolean deleteLinkSuppressed) {
+        innerObjectProperty.setDeleteLinkSuppressed(deleteLinkSuppressed);
+    }
 
     
 }

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

@@ -86,12 +86,13 @@ class ObjectPropertyStatementDaoFiltering extends BaseFiltering implements Objec
 	
     @Override
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
-            String subjectUri, String propertyUri, String objectKey, String rangeUri,
+            String subjectUri, String propertyUri, String objectKey, String domainUri, 
-            String query, Set<String> queryStrings, String sortDirection) {
+            String rangeUri, String query, Set<String> queryStrings, String sortDirection) {
         
         List<Map<String, String>> data = 
         	innerObjectPropertyStatementDao.getObjectPropertyStatementsForIndividualByProperty(
-        			subjectUri, propertyUri, objectKey, rangeUri, query, queryStrings,sortDirection);
+        			subjectUri, propertyUri, objectKey, domainUri, rangeUri, query, 
+        			        queryStrings,sortDirection);
         
         /* Filter the data
          * 
@@ -107,6 +108,7 @@ class ObjectPropertyStatementDaoFiltering extends BaseFiltering implements Objec
             ObjectPropertyStatement statement = new ObjectPropertyStatementImpl(subjectUri, propertyUri, objectUri);
             ObjectProperty op = new ObjectProperty();
             op.setURI(propertyUri);
+            op.setDomainVClassURI(domainUri);
             op.setRangeVClassURI(rangeUri);
             statement.setProperty(op);
             stmtsToData.put(statement, map);

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

@@ -834,7 +834,11 @@ public class JenaBaseDao extends JenaBaseDaoCon {
         try {                       
             String localName = r.getLocalName();
             if (localName != null) {
-                label = localName;
+                if(localName.trim().length() > 0) {
+                    label = localName;
+                } else {
+                    label = r.getURI();
+                }
             } else if (r.isAnon()) {
                 label = r.getId().toString();
             } else {
@@ -925,8 +929,10 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     			return null;
     		if (vitroURIStr.indexOf(PSEUDO_BNODE_NS)==0) {
     			String idStr = vitroURIStr.split("#")[1];
+    			log.debug("Trying to get bnode " + idStr);
     			RDFNode rdfNode = ontModel.getRDFNode(Node.createAnon(AnonId.create(idStr)));
     			if ( (rdfNode != null) && (rdfNode.canAs(OntClass.class)) ) {
+    			    log.debug("found it");
     				cls = rdfNode.as(OntClass.class);
     			}
 			} else {

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

@@ -75,6 +75,9 @@ public class JenaBaseDaoCon {
     protected AnnotationProperty PROPERTY_INPROPERTYGROUPANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_INPROPERTYGROUPANNOT);
     protected AnnotationProperty PROPERTY_COLLATEBYSUBCLASSANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_COLLATEBYSUBCLASSANNOT);
     protected AnnotationProperty PROPERTY_STUBOBJECTPROPERTYANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_STUBOBJECTPROPERTYANNOT);
+    protected AnnotationProperty PROPERTY_EDITLINKSUPPRESSED = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_EDITLINKSUPPRESSED);
+    protected AnnotationProperty PROPERTY_ADDLINKSUPPRESSED = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_ADDLINKSUPPRESSED);
+    protected AnnotationProperty PROPERTY_DELETELINKSUPPRESSED = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_DELETELINKSUPPRESSED);
     
     protected OntClass 		     PROPERTYGROUP = _constModel.createClass(VitroVocabulary.PROPERTYGROUP);
 

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

@@ -37,6 +37,7 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.sparql.expr.NodeValue;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
@@ -224,6 +225,13 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
             Boolean collateBySubclass = getPropertyBooleanValue(op,PROPERTY_COLLATEBYSUBCLASSANNOT);
             p.setCollateBySubclass(collateBySubclass==null ? false : collateBySubclass);
             
+            Boolean editLinkSuppressed = getPropertyBooleanValue(op, PROPERTY_EDITLINKSUPPRESSED);
+            p.setEditLinkSuppressed(editLinkSuppressed == null ? false : editLinkSuppressed);
+            Boolean addLinkSuppressed = getPropertyBooleanValue(op, PROPERTY_ADDLINKSUPPRESSED);
+            p.setAddLinkSuppressed(addLinkSuppressed == null ? false : addLinkSuppressed);
+            Boolean deleteLinkSuppressed = getPropertyBooleanValue(op, PROPERTY_DELETELINKSUPPRESSED);
+            p.setDeleteLinkSuppressed(deleteLinkSuppressed == null ? false : deleteLinkSuppressed);
+            
             Resource groupRes = (Resource) op.getPropertyValue(PROPERTY_INPROPERTYGROUPANNOT);
             if (groupRes != null) {
                 p.setGroupURI(groupRes.getURI());
@@ -284,21 +292,39 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         }
     }
     
-    public ObjectProperty getObjectPropertyByURIAndRangeURI(String propertyURI, String rangeURI) {
+    public ObjectProperty getObjectPropertyByURIs(String propertyURI, String domainURI, String rangeURI) {
+        if(log.isDebugEnabled()) {
+            log.debug("Getting " + propertyURI + " with domain " + domainURI + " and range " + rangeURI);
+        }
         ObjectProperty op = getObjectPropertyByURI(propertyURI);
-        if (op == null) {
+        if (op == null || rangeURI == null) {
             return op;
         }
+        op.setDomainVClassURI(domainURI);
         op.setRangeVClassURI(rangeURI);
         String propQuery = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
                 "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
                 "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
-                "SELECT ?range ?label ?group ?customForm ?displayLevel ?updateLevel WHERE { \n" +
+                "SELECT ?range ?label ?group ?customForm ?displayRank ?displayLevel " +
-                "    ?context config:configContextFor <" + propertyURI + "> . \n" +
+                "    ?updateLevel ?editLinkSuppressed ?addLinkSuppressed ?deleteLinkSuppressed \n" +
-                "    ?context config:qualifiedBy <" + rangeURI + "> . \n" +
+                " WHERE { \n" +
-                "    ?context config:hasConfiguration ?configuration . \n" +
+                "    ?context config:configContextFor <" + propertyURI + "> . \n";
+        if (domainURI != null) {
+                propQuery += "    ?context config:qualifiedByDomain <" + domainURI + "> . \n";
+        } else {
+                propQuery += "   FILTER NOT EXISTS { ?context config:qualifiedByDomain ?domainURI } \n";
+        }
+        if (rangeURI != null) {
+            propQuery += "    ?context config:qualifiedBy <" + rangeURI + "> . \n";
+        };
+                propQuery += "    ?context config:hasConfiguration ?configuration . \n" +
+                "    ?configuration a config:ObjectPropertyDisplayConfig . \n" +
                 "    OPTIONAL { ?configuration config:propertyGroup ?group } \n" +
                 "    OPTIONAL { ?configuration config:displayName ?label } \n" +
+                "    OPTIONAL { ?configuration config:editLinkSuppressed ?editLinkSuppressed } \n" +
+                "    OPTIONAL { ?configuration config:addLinkSuppressed ?addLinkSuppressed } \n" +
+                "    OPTIONAL { ?configuration config:deleteLinkSuppressed ?deleteLinkSuppressed } \n" +
+                "    OPTIONAL { ?configuration vitro:displayRankAnnot ?displayRank } \n" +
                 "    OPTIONAL { ?configuration vitro:customEntryFormAnnot ?customForm } \n" +
                 "    OPTIONAL { ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
                 "    OPTIONAL { ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n" +
@@ -314,6 +340,11 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 if (groupRes != null) {
                     op.setGroupURI(groupRes.getURI());
                 } 
+                Literal displayRankLit = qsoln.getLiteral("displayRank");
+                if(displayRankLit != null) {
+                    op.setDomainDisplayTier(
+                            Integer.parseInt(displayRankLit.getLexicalForm()));
+                } 
                 Resource displayLevelRes = qsoln.getResource("displayLevel");
                 if (displayLevelRes != null) {
                     op.setHiddenFromDisplayBelowRoleLevel(
@@ -334,6 +365,18 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 if (customFormLit != null) {
                     op.setCustomEntryForm(customFormLit.getLexicalForm());
                 } 
+                Literal editLinkSuppressedLit = qsoln.getLiteral("editLinkSuppressed");
+                if (editLinkSuppressedLit != null ) {
+                    op.setEditLinkSuppressed(editLinkSuppressedLit.getBoolean());
+                }
+                Literal addLinkSuppressedLit = qsoln.getLiteral("addLinkSuppressed");
+                if (addLinkSuppressedLit != null ) {
+                    op.setAddLinkSuppressed(addLinkSuppressedLit.getBoolean());
+                }
+                Literal deleteLinkSuppressedLit = qsoln.getLiteral("deleteLinkSuppressed");
+                if (deleteLinkSuppressedLit != null ) {
+                    op.setDeleteLinkSuppressed(deleteLinkSuppressedLit.getBoolean());
+                }
             }  
         } finally {
             qe.close();
@@ -902,14 +945,14 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     protected static final String LIST_VIEW_CONFIG_FILE_QUERY_STRING =
         "PREFIX display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> \n" +
         "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
-        "SELECT ?property ?range ?filename WHERE { \n" +
+        "SELECT ?property ?range ?domain ?filename WHERE { \n" +
         "    { ?property display:listViewConfigFile ?filename \n" +
         "    } UNION { \n" +
-        "        ?lv config:listViewConfigFile ?filename . \n " +
+        "        ?configuration config:listViewConfigFile ?filename . \n " +
-        "        ?configuration config:hasListView ?lv . " +
         "        ?context config:hasConfiguration ?configuration . \n" +
         "        ?context config:configContextFor ?property . \n" +
         "        ?context config:qualifiedBy ?range . \n" +
+        "        OPTIONAL { ?context config:qualifiedByDomain ?domain } \n" +
         "    } \n" +
         "}";
         
@@ -925,14 +968,15 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     
     //TODO private void addPropertyClassCombinationsToListViewMap(HashMap)    
     
-    // Map key is pair of object property and range class URI
+    // Map key is inner pair of object property and range class URI,
-    // If range is unspecified, OWL.Thing.getURI() is used in the key.
+    // with first member of outer pair being a domain class URI.
-    Map<Pair<ObjectProperty, String>, String> customListViewConfigFileMap = null;
+    // If domain or range is unspecified, OWL.Thing.getURI() is used in the key.
+    Map<Pair<String,Pair<ObjectProperty, String>>, String> customListViewConfigFileMap = null;
     
     @Override
     public String getCustomListViewConfigFileName(ObjectProperty op) {
         if (customListViewConfigFileMap == null) {
-            customListViewConfigFileMap = new HashMap<Pair<ObjectProperty, String>, String>();
+            customListViewConfigFileMap = new HashMap<Pair<String,Pair<ObjectProperty, String>>, String>();
             OntModel displayModel = getOntModelSelector().getDisplayModel();
             //Get all property to list view config file mappings in the system
             QueryExecution qexec = QueryExecutionFactory.create(listViewConfigFileQuery, displayModel); 
@@ -945,6 +989,10 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 String rangeUri = (rangeNode != null)
                         ? ((Resource) rangeNode).getURI()
                         : OWL.Thing.getURI();
+                RDFNode domainNode = soln.get("domain");
+                String domainUri = (domainNode != null)
+                        ? ((Resource) domainNode).getURI()
+                        : OWL.Thing.getURI();
                 ObjectProperty prop = getObjectPropertyByURI(propertyUri);
                 if (prop == null) {
                 	//This is a warning only if this property is the one for which we're searching
@@ -955,15 +1003,24 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 	}
                 } else {
                     String filename = soln.getLiteral("filename").getLexicalForm();
-                    customListViewConfigFileMap.put(new Pair<ObjectProperty, String>(prop, rangeUri), filename);     
+                    log.debug("putting " + domainUri + " " + prop.getURI() + " " + rangeUri + " " + filename + " into list view map");
+                    customListViewConfigFileMap.put(
+                            new Pair<String,Pair<ObjectProperty,String>>(
+                                    domainUri, new Pair<ObjectProperty, String>(
+                                            prop, rangeUri)), filename);     
                 }
             }       
             qexec.close();
         }      
         
-        String customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, op.getRangeVClassURI()));
+        String customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<String, Pair<ObjectProperty, String>>(op.getDomainVClassURI(), new Pair<ObjectProperty,String>(op, op.getRangeVClassURI())));
         if (customListViewConfigFileName == null) {
-            customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, OWL.Thing.getURI()));
+            log.debug("no list view found for " + op.getURI() + " qualified by range " + op.getRangeVClassURI() + " and domain " + op.getDomainVClassURI());
+            customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<String, Pair<ObjectProperty, String>>(OWL.Thing.getURI(), new Pair<ObjectProperty,String>(op, op.getRangeVClassURI())));
+        }
+        if (customListViewConfigFileName == null) {
+            log.debug("no list view found for " + op.getURI() + " qualified by range " + op.getRangeVClassURI());
+            customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<String, Pair<ObjectProperty, String>>(OWL.Thing.getURI(), new Pair<ObjectProperty,String>(op, OWL.Thing.getURI())));
         }
         
         return customListViewConfigFileName;

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

@@ -273,8 +273,7 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
             String subjectUri, 
             String propertyUri,             
-            String objectKey, 
+            String objectKey, String domainUri, String rangeUri,
-            String rangeUri,
             String queryString, 
             Set<String> constructQueryStrings,
             String sortDirection) {    	        
@@ -282,11 +281,13 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         Model constructedModel = constructModelForSelectQueries(
                 subjectUri, propertyUri, constructQueryStrings);
                     
+        if(log.isDebugEnabled()) {
+            log.debug("Constructed model has " + constructedModel.size() + " statements.");
+        }
+        
     	if("desc".equalsIgnoreCase( sortDirection ) ){
     		queryString = queryString.replaceAll(" ASC\\(", " DESC(");
     	}
-    	
-        log.debug("Query string for object property " + propertyUri + ": " + queryString);
         
         Query query = null;
         try {
@@ -300,10 +301,15 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         QuerySolutionMap initialBindings = new QuerySolutionMap();
         initialBindings.add("subject", ResourceFactory.createResource(subjectUri));
         initialBindings.add("property", ResourceFactory.createResource(propertyUri));
-        if (rangeUri != null) {
+        if (domainUri != null && !domainUri.startsWith(VitroVocabulary.PSEUDO_BNODE_NS)) {
+            initialBindings.add("subjectType", ResourceFactory.createResource(domainUri));
+        }
+        if (rangeUri != null && !rangeUri.startsWith(VitroVocabulary.PSEUDO_BNODE_NS)) {
             initialBindings.add("objectType", ResourceFactory.createResource(rangeUri));
         }
         
+        log.debug("Query string for object property " + propertyUri + ": " + queryString);
+        
         // Run the SPARQL query to get the properties
         List<Map<String, String>> list = new ArrayList<Map<String, String>>();
         DatasetWrapper w = dwf.getDatasetWrapper();
@@ -353,13 +359,13 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         Model constructedModel = ModelFactory.createDefaultModel();                        
         
         for (String queryString : constructQueries) {
+                     
+            queryString = queryString.replace("?subject", "<" + subjectUri + ">");
+            queryString = queryString.replace("?property", "<" + propertyUri + ">");
          
             log.debug("CONSTRUCT query string for object property " + 
                     propertyUri + ": " + queryString);
             
-            queryString = queryString.replace("?subject", "<" + subjectUri + ">");
-            queryString = queryString.replace("?property", "<" + propertyUri + ">");
-                       
             // we no longer need this query object, but we might want to do this
             // query parse step to improve debugging, depending on the error returned
             // through the RDF API

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

@@ -16,6 +16,7 @@ import java.util.Set;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.ontology.IntersectionClass;
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntProperty;
@@ -33,6 +34,7 @@ import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
+import com.hp.hpl.jena.sdb.util.Pair;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
 import com.hp.hpl.jena.vocabulary.OWL;
@@ -51,7 +53,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	
 	protected static final Log log = LogFactory.getLog(PropertyDaoJena.class.getName());
-
+	protected static final String FAUX_PROPERTY_FLAG = "FAUX";
+	
     private static final Map<String, String> NAMESPACES = new HashMap<String, String>() {{
         put("afn", VitroVocabulary.AFN);
         put("owl", VitroVocabulary.OWL);
@@ -328,7 +331,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
     public List <VClass> getClassesWithRestrictionOnProperty(String propertyURI) {
     	
     	if (propertyURI == null) {
-    		log.info("getClassesWithRestrictionOnProperty: called with null propertyURI");
+    		log.warn("getClassesWithRestrictionOnProperty: called with null propertyURI");
     		return null;
     	}
     	    	
@@ -348,7 +351,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 				   Statement statement = stmtIter.next();
 				   
 				   if ( statement.getSubject().canAs(OntClass.class) ) {
-					   classURISet.addAll(getRelatedClasses(statement.getSubject().as(OntClass.class)));
+					   classURISet.addAll(getRestrictedClasses(statement.getSubject().as(OntClass.class)));
 				   } else {
 					   log.warn("getClassesWithRestrictionOnProperty: Unexpected use of onProperty: it is not applied to a class");
 				   }
@@ -381,9 +384,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
     }
 
 	/**
-	 * Finds all named superclasses, subclasses and equivalent classes of
+	 * Find named classes to which a restriction "applies"
-	 * the given class.
-	 *
 	 * @param   resourceURI  identifier of a class
 	 * @return  set of class URIs
 	 * 
@@ -391,13 +392,12 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	 * the ontology model.
 	 */
 
-    public HashSet<String> getRelatedClasses(OntClass ontClass) {
+    public HashSet<String> getRestrictedClasses(OntClass ontClass) {
     	
         HashSet<String> classSet = new HashSet<String>();
   
         List<OntClass> classList = ontClass.listEquivalentClasses().toList();
         classList.addAll(ontClass.listSubClasses().toList());
-        classList.addAll(ontClass.listSuperClasses().toList());
         
         Iterator<OntClass> it = classList.iterator();
 		         
@@ -406,6 +406,8 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         	
         	if (!oc.isAnon()) {
         		classSet.add(oc.getURI());
+        	} else {
+        	    classSet.addAll(getRestrictedClasses(oc));
         	}
         }
         		
@@ -524,15 +526,8 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
             }
         }
     	
-    	List<PropertyInstance> piList = getAllPropInstByVClasses(vclasses);
+    	return getAllPropInstByVClasses(vclasses);
     	
-    	for (PropertyInstance pi : piList) {
-    		pi.setDomainClassURI(ind.getVClassURI());
-    		// TODO: improve.  This is so the DWR property editing passes the 
-    		// individual's VClass to get the right restrictions
-    	}
-
-		return piList;
     }
     
     /*
@@ -621,6 +616,42 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         return classes;
     }
     
+    private static final int DEPTH_LIMIT = 20;
+    
+    private List<Restriction> getRelatedRestrictions(OntClass ontClass) {
+        return getRelatedRestrictions(ontClass, new ArrayList<Restriction>(), DEPTH_LIMIT);
+    }
+    
+    private List<Restriction> getRelatedRestrictions(OntClass ontClass, 
+            List<Restriction> relatedRestrictions, int limit) {
+        limit--;
+        if (ontClass.isRestriction()) {
+            relatedRestrictions.add(ontClass.as(Restriction.class));
+        } else if (ontClass.isIntersectionClass()) {
+            IntersectionClass inter = ontClass.as(IntersectionClass.class);
+            Iterator<? extends OntClass> operIt = inter.listOperands();
+            while (operIt.hasNext()) {
+                OntClass operand = operIt.next();
+                if (!relatedRestrictions.contains(operand) && limit > 0) {
+                    relatedRestrictions.addAll(
+                            getRelatedRestrictions(
+                                    operand, relatedRestrictions, limit));
+                }
+            }   
+        } else {
+            List<OntClass> superClasses = listSuperClasses(ontClass);
+            superClasses.addAll(listEquivalentClasses(ontClass));
+            for (OntClass sup : superClasses) {
+                if (sup.isAnon() && !sup.equals(ontClass) 
+                        && !relatedRestrictions.contains(ontClass) && limit > 0) {
+                    relatedRestrictions.addAll(
+                            getRelatedRestrictions(sup, relatedRestrictions, limit));
+                }
+            }
+        }
+        return relatedRestrictions;
+    }
+    
     public List<PropertyInstance> getAllPropInstByVClasses(List<VClass> vclasses) {
         
         List<PropertyInstance> propInsts = new ArrayList<PropertyInstance>();
@@ -651,55 +682,52 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 		            String VClassURI = vclass.getURI();
 		            
 		        	OntClass ontClass = getOntClass(ontModel,VClassURI);
-		        	if (ontClass != null) {
+		        	if (ontClass == null) {
-		        	    List<OntClass> relatedClasses = new ArrayList<OntClass>();
+		        	    continue;  
-		        	    relatedClasses.addAll(listEquivalentClasses(ontClass));		        	    
-		        	    relatedClasses.addAll(listSuperClasses(ontClass));
-		        	    for (OntClass relatedClass : relatedClasses) {
-    		        	    // find properties in restrictions
-    		        		if (relatedClass.isRestriction() && relatedClass.canAs(Restriction.class)) {
-    		        			// TODO: check if restriction is something like
-    		        			// maxCardinality 0 or allValuesFrom owl:Nothing,
-    		        			// in which case the property is NOT applicable!
-    		        			Restriction rest = relatedClass.as(Restriction.class);
-    		        			OntProperty onProperty = rest.getOnProperty();
-    		        			if (onProperty != null) {
-    		        			    Resource[] ranges = new Resource[2];
-    		        			    if (rest.isAllValuesFromRestriction()) {
-    		        			        ranges[0] = (rest.asAllValuesFromRestriction()).getAllValuesFrom();
-    		        			    } else if (rest.isSomeValuesFromRestriction()) {
-                                        ranges[1] = (rest.asSomeValuesFromRestriction()).getSomeValuesFrom();
-                                    }
-    		        				updatePropertyRangeMap(applicableProperties, onProperty.getURI(), ranges);
-    		        			}
-    		        		}
-		        	    }
-		        		
-		        	    List<Resource> propertyList = 
-		        	    	    getPropertiesWithAppropriateDomainFor(VClassURI);
-		        		for (Resource prop : propertyList) {
-		        		    if (prop.getNameSpace() != null 
-		        		            && !NONUSER_NAMESPACES.contains(
-		        		                    prop.getNameSpace()) ) {
-		        		        StmtIterator rangeSit = prop.listProperties(
-		        		                RDFS.range);
-		        		        Resource rangeRes = null;
-		        		        while (rangeSit.hasNext()) {    
-		        		            Statement s = rangeSit.nextStatement();
-		        		            if (s.getObject().isURIResource()) {
-		        		                rangeRes = (Resource) s.getObject();
-		        		            }
-		        		        }
-		        		        Resource[] ranges = new Resource[2];
-		        		        ranges[0] = rangeRes;
-		        		        updatePropertyRangeMap(
-		        		                applicableProperties, prop.getURI(), ranges);
-		        		        
-		        		    }
-		        		}
-		        		
 		        	}
-		        }       
+	        	    List<Restriction> relatedRestrictions = getRelatedRestrictions(ontClass);
+	        	    for (Restriction rest : relatedRestrictions) {
+		        	    // find properties in restrictions
+	        			// TODO: check if restriction is something like
+	        			// maxCardinality 0 or allValuesFrom owl:Nothing,
+	        			// in which case the property is NOT applicable!
+	        			OntProperty onProperty = rest.getOnProperty();
+	        			if (onProperty != null) {
+	        			    Resource[] ranges = new Resource[2];
+	        			    if (rest.isAllValuesFromRestriction()) {
+	        			        ranges[0] = (rest.asAllValuesFromRestriction()).getAllValuesFrom();
+	        			    } else if (rest.isSomeValuesFromRestriction()) {
+                                ranges[1] = (rest.asSomeValuesFromRestriction()).getSomeValuesFrom();
+                            }
+	        				updatePropertyRangeMap(applicableProperties, onProperty.getURI(), ranges);
+		        		}
+	        	    }
+	        		
+	        	    List<Resource> propertyList = 
+	        	    	    getPropertiesWithAppropriateDomainFor(VClassURI);
+	        		for (Resource prop : propertyList) {
+	        		    if (prop.getNameSpace() != null 
+	        		            && !NONUSER_NAMESPACES.contains(
+	        		                    prop.getNameSpace()) ) {
+	        		        StmtIterator rangeSit = prop.listProperties(
+	        		                RDFS.range);
+	        		        Resource rangeRes = null;
+	        		        while (rangeSit.hasNext()) {    
+	        		            Statement s = rangeSit.nextStatement();
+	        		            if (s.getObject().isURIResource()) {
+	        		                rangeRes = (Resource) s.getObject();
+	        		            }
+	        		        }
+	        		        Resource[] ranges = new Resource[2];
+	        		        ranges[0] = rangeRes;
+	        		        updatePropertyRangeMap(
+	        		                applicableProperties, prop.getURI(), ranges);
+	        		        
+	        		    }
+	        		}
+	        		
+	        	}
+		             
         	} catch (Exception e) {
         		log.error("Unable to get applicable properties " +
         		          "by examining property restrictions and domains", e);
@@ -718,12 +746,36 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	                            : (op.getRange() == null && foundRanges[1] != null)
 	                            ? foundRanges[1]
 	                                    : op.getRange();
-	                            propInsts.add(getPropInstForPropertyAndRange(op, rangeRes, applicableProperties));
+	            Resource domainRes = op.getDomain();
-	            List<String> additionalFauxSubpropertyRangeURIs = getAdditionalFauxSubpropertyRangeURIsForPropertyURI(propertyURI);
+	                            propInsts.add(getPropInst(
-	            for (String rangeURI : additionalFauxSubpropertyRangeURIs) {
+	                                    op, domainRes, rangeRes, applicableProperties));
-	                if (getWebappDaoFactory().getVClassDao().isSubClassOf(rangeURI, rangeRes.getURI())) {
+	            List<Pair<String,String>> additionalFauxSubpropertyDomainAndRangeURIs = 
-	                    propInsts.add(getPropInstForPropertyAndRange(
+	                    getAdditionalFauxSubpropertyDomainAndRangeURIsForPropertyURI(
-	                            op, ResourceFactory.createResource(rangeURI), applicableProperties));
+	                            propertyURI);
+	            for (Pair<String,String> domainAndRangeURIs : 
+	                    additionalFauxSubpropertyDomainAndRangeURIs) {
+	                boolean applicablePropInst = false;
+	                if (rangeRes == null ||  
+	                        !getWebappDaoFactory().getVClassDao().isSubClassOf(
+	                            rangeRes.getURI(), domainAndRangeURIs.getRight())) { 
+	                    if (domainAndRangeURIs.getLeft() == null) {
+	                        applicablePropInst = true;
+	                    } else {
+    	                    for(VClass vclass : vclasses) {
+    	                        if (vclass.getURI() != null && vclass.getURI().equals(
+    	                                domainAndRangeURIs.getLeft())) {
+    	                            applicablePropInst = true;
+    	                            break;
+    	                        }
+    	                    }
+	                    }
+	                    if (applicablePropInst) {
+    	                    propInsts.add(getPropInst(
+                                    op,
+                                    ResourceFactory.createResource(domainAndRangeURIs.getLeft()),
+                                    ResourceFactory.createResource(domainAndRangeURIs.getRight()), 
+                                    applicableProperties));
+	                    }
 	                }
 	            }
 	        }
@@ -736,11 +788,19 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         
     }
     
-    private PropertyInstance getPropInstForPropertyAndRange(OntProperty op, Resource rangeRes, 
+    private PropertyInstance getPropInst(OntProperty op, Resource domainRes, Resource rangeRes, 
-                                                              Map<String, Resource[]> applicableProperties) {                   
+                                                              Map<String, Resource[]> applicableProperties) {  
+        if (log.isDebugEnabled() && domainRes != null && rangeRes != null) {
+            log.debug("getPropInst() op: " + op.getURI() + " domain: " + 
+                domainRes.getURI() + " range: " + rangeRes.getURI());
+        }
         PropertyInstance pi = new PropertyInstance();
-        String domainURIStr = getURIStr(op.getDomain());
+        String domainURIStr = (domainRes != null && !domainRes.isAnon()) ? 
-        if (rangeRes != null) {
+                domainURIStr = domainRes.getURI()
+                : null;
+        if (rangeRes == null) {
+            pi.setRangeClassURI(OWL.Thing.getURI()); // TODO see above
+        } else {
             String rangeClassURI;
             if (rangeRes.isAnon()) {
                 rangeClassURI = PSEUDO_BNODE_NS + rangeRes.getId()
@@ -757,18 +817,18 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
                 range.setName(range.getLocalName());
             }
             pi.setRangeClassName(range.getName());
-        } else {
-            pi.setRangeClassURI(OWL.Thing.getURI()); // TODO see above
         }
         pi.setDomainClassURI(domainURIStr);
-        VClass domain = getWebappDaoFactory().getVClassDao()
+        if (domainURIStr != null) {
-                .getVClassByURI(domainURIStr);
+            VClass domain = getWebappDaoFactory().getVClassDao()
-        if (domain == null) {
+                    .getVClassByURI(domainURIStr);
-            domain = new VClass();
+            if (domain == null) {
-            domain.setURI(domainURIStr);
+                domain = new VClass();
-            domain.setName(domain.getLocalName());
+                domain.setURI(domainURIStr);
+                domain.setName(domain.getLocalName());
+            }
+            pi.setDomainClassName(domain.getName());
         }
-        pi.setDomainClassName(domain.getName());
         pi.setSubjectSide(true);
         pi.setPropertyURI(op.getURI());
         pi.setPropertyName(getLabelOrId(op)); // TODO
@@ -777,14 +837,15 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         return pi;
     }
     
-    private List<String> getAdditionalFauxSubpropertyRangeURIsForPropertyURI(String propertyURI) {
+    private List<Pair<String,String>> getAdditionalFauxSubpropertyDomainAndRangeURIsForPropertyURI(String propertyURI) {
-        List<String> rangeURIs = new ArrayList<String>();
+        List<Pair<String,String>> domainAndRangeURIs = new ArrayList<Pair<String,String>>();
         String propQuery = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
                 "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
                 "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
-                "SELECT ?range WHERE { \n" +
+                "SELECT ?domain ?range WHERE { \n" +
                 "    ?context config:configContextFor <" + propertyURI + "> . \n" +
                 "    ?context config:qualifiedBy ?range . \n" +
+                "    OPTIONAL { ?context config:qualifiedByDomain ?domain } \n" +
                 "}"; 
 
         Query q = QueryFactory.create(propQuery);
@@ -794,12 +855,18 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
             while (rs.hasNext()) {
                 QuerySolution qsoln = rs.nextSolution();
                 Resource rangeRes = qsoln.getResource("range");
-                rangeURIs.add(rangeRes.getURI());
+                String rangeURI = rangeRes.getURI();
+                Resource domainRes = qsoln.getResource("domain");
+                String domainURI = null;
+                if (domainRes != null && !domainRes.isAnon()) {
+                    domainURI = domainRes.getURI();
+                } 
+                domainAndRangeURIs.add(new Pair<String,String>(domainURI, rangeURI));
             }  
         } finally {
             qe.close();
         }
-        return rangeURIs;
+        return domainAndRangeURIs;
     }
 
     private String getURIStr(Resource res) {

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

@@ -462,9 +462,11 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                 while (classIt.hasNext()) {
                     try {
                         Individual classInd = classIt.next();
-                        OntClass cls = classInd.as(OntClass.class);
+                        if(classInd.canAs(OntClass.class)) {
-                        if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) {
+                            OntClass cls = classInd.as(OntClass.class);
-                            classes.add(new VClassJena(cls,getWebappDaoFactory()));
+                            if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) {
+                                classes.add(new VClassJena(cls,getWebappDaoFactory()));
+                            }
                         }
                     } catch (ClassCastException cce) {
                         log.error(cce, cce);
@@ -1091,11 +1093,8 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         OntModel ontModel = getOntModel();
         try {
             ontModel.enterCriticalSection(Lock.READ);
-            OntClass oc1 = getOntClass(ontModel, vclassURI1);
+            Resource oc1 = ontModel.getResource(vclassURI1);
-            OntClass oc2 = getOntClass(ontModel, vclassURI2);
+            Resource oc2 = ontModel.getResource(vclassURI2);
-            if (oc1 == null || oc2 == null) {
-                return false;
-            } 
             return ontModel.contains(oc1, RDFS.subClassOf, oc2);
         } finally {
             ontModel.leaveCriticalSection();

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

@@ -2,10 +2,15 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
+import java.util.ArrayList;
+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.OntClass;
+import com.hp.hpl.jena.ontology.UnionClass;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.Statement;
@@ -376,4 +381,27 @@ public class VClassJena extends VClass {
             }
         }		 	                      
     }
+    
+    @Override
+    public boolean isUnion() {
+        return this.cls.isUnionClass();
+    }
+    
+    //TODO consider anonymous components
+    @Override
+    public List<VClass> getUnionComponents() {
+        List<VClass> unionComponents = new ArrayList<VClass>();
+        if (isUnion()) {
+            UnionClass union = this.cls.as(UnionClass.class);
+            Iterator<? extends OntClass> opIt = union.listOperands();
+            while(opIt.hasNext()) {
+                OntClass component = opIt.next();
+                if (!component.isAnon()) {
+                    unionComponents.add(new VClassJena(component, this.webappDaoFactory));  
+                }
+            }
+        }
+        return unionComponents;
+    }
+    
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/pellet/PelletListener.java

@@ -624,8 +624,10 @@ public class PelletListener implements ModelChangedListener {
 				if ( (additionModel.size() > 0) || (removalModel.size()>0) ) {
 					if (!isSynchronizing) {
 						if (foreground) {
+                            log.debug("Running Pellet in foreground.");
 							(new PelletSynchronizer()).run();
 						} else {
+                            log.debug("Running Pellet in background.");
 							new Thread(new PelletSynchronizer(), "PelletListener.PelletSynchronizer").start();
 						}
 					}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/pellet/ReasonerConfiguration.java

@@ -30,8 +30,7 @@ public class ReasonerConfiguration {
 	/**
 	 * The default reasoner configuration is designed to provide acceptable performance on larger knowledge bases.
 	 * It will classify and realize, and add inferred disjointWith statements.
-	 * It ignores domain and range "axioms," on the assumption that they are not truly axioms but editing constraints.
+	 * It ignores domain and range "axioms," on the assumption that they are not truly axioms but editing constraints.  
-	 * It also ignores "owl:inverseOf."  
 	 */
 	public static ReasonerConfiguration DEFAULT;
 	
@@ -78,6 +77,7 @@ public class ReasonerConfiguration {
         defaultInferenceDrivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,RDF.first,null));
         defaultInferenceDrivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,RDF.rest,null));
         defaultInferenceDrivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,OWL.disjointWith,null));
+        defaultInferenceDrivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,OWL.inverseOf,null));
         DEFAULT.setInferenceDrivingPatternAllowSet(defaultInferenceDrivingPatternAllowSet);
         Set<ObjectPropertyStatementPattern> defaultInferenceReceivingPatternAllowSet = new HashSet<ObjectPropertyStatementPattern>();
         defaultInferenceReceivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,RDF.type,null));

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/EditConfigurationUtils.java

@@ -53,12 +53,22 @@ public class EditConfigurationUtils {
     	return vreq.getParameter("objectUri");
     }
     
+    public static String getDomainUri(VitroRequest vreq) {
+        return vreq.getParameter("domainUri");
+    }
+    
     public static String getRangeUri(VitroRequest vreq) {
         return vreq.getParameter("rangeUri");
     }
     
     public static VClass getRangeVClass(VitroRequest vreq) {
-        return vreq.getWebappDaoFactory().getVClassDao().getVClassByURI(getRangeUri(vreq));
+        // This needs a WebappDaoFactory with no filtering/RDFService
+        // funny business because it needs to be able to retrieve anonymous union
+        // classes by their "pseudo-bnode URIs".
+        // Someday we'll need to figure out a different way of doing this.
+        WebappDaoFactory ctxDaoFact = ModelAccess.on(
+                vreq.getSession().getServletContext()).getWebappDaoFactory();
+        return ctxDaoFact.getVClassDao().getVClassByURI(getRangeUri(vreq));
     }
     
     //get individual

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/fields/IndividualsViaObjectPropetyOptions.java

@@ -27,13 +27,13 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
     private static final String LEFT_BLANK = "";
     private String subjectUri;
     private String predicateUri;    
-    private String rangeUri;
+    private List<VClass> rangeTypes;
     private String objectUri;
     
     private String defaultOptionLabel;
     
     public IndividualsViaObjectPropetyOptions(String subjectUri,
-            String predicateUri, String rangeUri, String objectUri) throws Exception {
+            String predicateUri, List<VClass> rangeTypes, String objectUri) throws Exception {
         super();
         
         if (subjectUri == null || subjectUri.equals("")) {
@@ -45,7 +45,7 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
 
         this.subjectUri = subjectUri;
         this.predicateUri = predicateUri;
-        this.rangeUri = rangeUri;
+        this.rangeTypes = rangeTypes;
         this.objectUri = objectUri;
     }
     
@@ -78,8 +78,8 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
         //get all vclasses applicable to the individual subject
         HashSet<String> vclassesURIs = getApplicableVClassURIs(subject, wDaoFact);
         
-        if (rangeUri != null) {
+        if (!rangeTypes.isEmpty()) {
-            vclassesURIs = filterToSubclassesOfRange(vclassesURIs, rangeUri, wDaoFact);
+            vclassesURIs = filterToSubclassesOfRange(vclassesURIs, rangeTypes, wDaoFact);
         }
                 
         if (vclassesURIs.size() == 0) {           
@@ -117,9 +117,13 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
 
     private HashSet<String> getApplicableVClassURIs(Individual subject, WebappDaoFactory wDaoFact) {
         HashSet<String> vclassesURIs = new HashSet<String>();
-        if (rangeUri != null) {
+        if (!rangeTypes.isEmpty()) {
-            log.debug("individualsViaObjectProperty using rangeUri " + rangeUri);
+            StringBuffer rangeBuff = new StringBuffer();
-            vclassesURIs.add(rangeUri);
+            for (VClass rangeType : rangeTypes) {
+                vclassesURIs.add(rangeType.getURI());
+                rangeBuff.append(rangeType.getURI()).append(", ");
+            }
+            log.debug("individualsViaObjectProperty using rangeUri " + rangeBuff.toString());            
             return vclassesURIs;
         } 
         
@@ -144,13 +148,15 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
     }
     
     private HashSet<String> filterToSubclassesOfRange(HashSet<String> vclassesURIs, 
-                                              String rangeUri, 
+                                              List<VClass> rangeTypes, 
                                               WebappDaoFactory wDaoFact) {
         HashSet<String> filteredVClassesURIs = new HashSet<String>();
         VClassDao vcDao = wDaoFact.getVClassDao();
         for (String vclass : vclassesURIs) {
-            if (vclass.equals(rangeUri) || vcDao.isSubClassOf(vclass, rangeUri)) {
+            for (VClass rangeType : rangeTypes) {
-                filteredVClassesURIs.add(vclass);
+                if (vclass.equals(rangeType.getURI()) || vcDao.isSubClassOf(vclass, rangeType.getURI())) {
+                    filteredVClassesURIs.add(vclass);
+                }
             }
         }
         return filteredVClassesURIs;

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DefaultObjectPropertyFormGenerator.java

@@ -99,41 +99,60 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
     	return getDefaultObjectEditConfiguration(vreq, session);
     }
 	
-    protected List<String> getRangeTypes(VitroRequest vreq) {
+    protected List<VClass> getRangeTypes(VitroRequest vreq) {
-        WebappDaoFactory wDaoFact = vreq.getWebappDaoFactory();
+        // This first part needs a WebappDaoFactory with no filtering/RDFService
-        List<String> types = new ArrayList<String>();
+        // funny business because it needs to be able to retrieve anonymous union
+        // classes by their "pseudo-bnode URIs".
+        // Someday we'll need to figure out a different way of doing this.
+        WebappDaoFactory ctxDaoFact = ModelAccess.on(
+                vreq.getSession().getServletContext()).getWebappDaoFactory();
+        List<VClass> types = new ArrayList<VClass>();
     	Individual subject = EditConfigurationUtils.getSubjectIndividual(vreq);
    		String predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
    		String rangeUri = EditConfigurationUtils.getRangeUri(vreq);
    		if (rangeUri != null) {
-   		    types.add(rangeUri);
+   		    VClass rangeVClass = ctxDaoFact.getVClassDao().getVClassByURI(rangeUri);
+   		    if (!rangeVClass.isUnion()) {
+   		        types.add(rangeVClass);    
+   		    } else {
+   		        for (VClass unionComponent : rangeVClass.getUnionComponents()) {
+   		            types.add(unionComponent);
+   		        }
+   		    }
 	        return types;
    		}
+   		WebappDaoFactory wDaoFact = vreq.getWebappDaoFactory();
 		//Get all vclasses applicable to subject
 		List<VClass> vClasses = subject.getVClasses();
-		HashSet<String> typesHash = new HashSet<String>();
+		HashMap<String, VClass> typesHash = new HashMap<String, VClass>();
 		for(VClass vclass: vClasses) {
 			 List<VClass> rangeVclasses = wDaoFact.getVClassDao().getVClassesForProperty(vclass.getURI(),predicateUri);
 			 if(rangeVclasses !=  null) {
 				 for(VClass range: rangeVclasses) {
 					 //a hash will keep a unique list of types and so prevent duplicates
-					 typesHash.add(range.getURI());
+					 typesHash.put(range.getURI(), range);
 				 }
 			 }
 		}
-		types.addAll(typesHash);
+		types.addAll(typesHash.values());
         return types;
 	}	
 	
     private boolean tooManyRangeOptions(VitroRequest vreq, HttpSession session ) throws SolrServerException {
-    	List<String> types = getRangeTypes(vreq);
+    	List<VClass> rangeTypes = getRangeTypes(vreq);
     	SolrServer solrServer = SolrSetup.getSolrServer(session.getServletContext());
     	
+    	List<String> types = new ArrayList<String>();
     	//empty list means the range is not set to anything, force Thing
-    	if(types.size() == 0 ){
+        if(types.size() == 0 ){
-    		types = new ArrayList<String>();
+            types.add(VitroVocabulary.OWL_THING);
-    		types.add(VitroVocabulary.OWL_THING);
+        } else { 
-    	}
+        	for (VClass vclass : rangeTypes) {
+        	    if (vclass.getURI() != null) {
+        	        types.add(vclass.getURI());
+        	    }
+        	}
+        }
     	
     	long count = 0;    		   
     	for( String type:types){
@@ -184,7 +203,7 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
     	this.setSparqlQueries(editConfiguration);
     	
     	//set fields
-    	setFields(editConfiguration, vreq, EditConfigurationUtils.getPredicateUri(vreq), EditConfigurationUtils.getRangeUri(vreq));
+    	setFields(editConfiguration, vreq, EditConfigurationUtils.getPredicateUri(vreq), getRangeTypes(vreq));
     	
     //	No need to put in session here b/c put in session within edit request dispatch controller instead
     	//placing in session depends on having edit key which is handled in edit request dispatch controller
@@ -358,7 +377,7 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
         setFields(editConfiguration, vreq, predicateUri, null);
     }
     
-    protected void setFields(EditConfigurationVTwo editConfiguration, VitroRequest vreq, String predicateUri, String rangeUri) throws Exception {
+    protected void setFields(EditConfigurationVTwo editConfiguration, VitroRequest vreq, String predicateUri, List<VClass> rangeTypes) throws Exception {
 		FieldVTwo field = new FieldVTwo();
     	field.setName("objectVar");    	
     	
@@ -370,7 +389,7 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
     		field.setOptions( new IndividualsViaObjectPropetyOptions(
     	        subjectUri, 
     	        predicateUri,
-    	        rangeUri,
+    	        rangeTypes,
     	        objectUri));
     	}else{
     		field.setOptions(null);
@@ -441,14 +460,22 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
 		formSpecificData.put("editMode", getEditMode(vreq).toString().toLowerCase());
 		
 		//We also need the type of the object itself
-		List<String> types = getRangeTypes(vreq);
+		List<VClass> types = getRangeTypes(vreq);
         //if types array contains only owl:Thing, the search will not return any results
         //In this case, set an empty array
-        if(types.size() == 1 && types.get(0).equals(VitroVocabulary.OWL_THING) ){
+        if(types.size() == 1 && types.get(0).getURI().equals(VitroVocabulary.OWL_THING) ){
-        	types = new ArrayList<String>();
+        	types = new ArrayList<VClass>();
         }
 		
-		formSpecificData.put("objectTypes", StringUtils.join(types, ","));
+        StringBuffer typesBuff = new StringBuffer();
+        for (VClass type : types) {
+            if (type.getURI() != null) {
+                typesBuff.append(type.getURI()).append(",");
+            }
+        }
+        
+		formSpecificData.put("objectTypes", typesBuff.toString());
+		log.debug("autocomplete object types : "  + formSpecificData.get("objectTypes"));
 		
 		//Get label for individual if it exists
 		if(EditConfigurationUtils.getObjectIndividual(vreq) != null) {
@@ -464,15 +491,15 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
 		editConfiguration.setFormSpecificData(formSpecificData);
 	}
 	
-	private Object rangeIndividualsExist(HttpSession session, List<String> types) throws SolrServerException {		
+	private Object rangeIndividualsExist(HttpSession session, List<VClass> types) throws SolrServerException {		
     	SolrServer solrServer = SolrSetup.getSolrServer(session.getServletContext());
     	
     	boolean rangeIndividualsFound = false;
-    	for( String type:types){
+    	for( VClass type:types){
     		//solr for type count.
     		SolrQuery query = new SolrQuery();   
     		
-    		query.setQuery( VitroSearchTermNames.RDFTYPE + ":" + type);
+    		query.setQuery( VitroSearchTermNames.RDFTYPE + ":" + type.getURI());
     		query.setRows(0);
     		
     		QueryResponse rsp = solrServer.query(query);

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsForIndividualGenerator.java

@@ -28,8 +28,10 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestActio
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AddDataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AddObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@@ -272,7 +274,7 @@ public class ManageLabelsForIndividualGenerator extends BaseEditConfigurationGen
 				RequestActionConstants.SOME_URI);
 		AddObjectPropertyStatement aops = new AddObjectPropertyStatement(
 				vreq.getJenaOntModel(), individual.getURI(),
-				RequestActionConstants.SOME_URI,
+				RequestActionConstants.SOME_PREDICATE,
 				RequestActionConstants.SOME_URI);
     	return PolicyHelper.isAuthorizedForActions(vreq, new Actions(adps).or(aops));
 	}
@@ -317,8 +319,8 @@ public class ManageLabelsForIndividualGenerator extends BaseEditConfigurationGen
 				//This should put the label in the list
 				//Create label information instance with the required information
 				//To generate link
-				DataPropertyStatementTemplateModel dpstm = new DataPropertyStatementTemplateModel(subjectUri, propertyUri, l,
+				DataPropertyStatementTemplateModel dpstm = new DataPropertyStatementTemplateModel(
-			            template, vreq);
+				        subjectUri, new Property(propertyUri), l, template, vreq);
 				labelsList.add(new LabelInformation(
 						l, dpstm.getEditUrl(), dpstm.getDeleteUrl(), languageTag, languageName));
 			}

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/controller/EditRequestDispatchController.java

@@ -171,6 +171,9 @@ public class EditRequestDispatchController extends FreemarkerHttpServlet {
     	    	    makeEditConfigurationVTwo( editConfGeneratorName, vreq, session);
     	}
     	 
+    	if(editConfig == null) {
+    	    log.error("editConfig is null! How did this happen?");
+    	}
     	String editKey = EditConfigurationUtils.getEditKey(vreq); 
     	editConfig.setEditKey(editKey);        
         
@@ -199,6 +202,7 @@ public class EditRequestDispatchController extends FreemarkerHttpServlet {
 	    String editConfGeneratorName = null;
 	    
 	    String predicateUri =  getPredicateUri(vreq);
+	    String domainUri = EditConfigurationUtils.getDomainUri(vreq);
 	    String rangeUri = EditConfigurationUtils.getRangeUri(vreq);
 	    
         // *** handle the case where the form is specified as a request parameter ***	    
@@ -215,9 +219,9 @@ public class EditRequestDispatchController extends FreemarkerHttpServlet {
 
       	// *** check for a predicate URI in the request        	
         }else if( predicateUri != null && !predicateUri.isEmpty() ){                      
-            Property prop = getProperty( predicateUri, vreq);
+            Property prop = getProperty( predicateUri, domainUri, rangeUri, vreq);
             if (prop != null && rangeUri != null) {
-                editConfGeneratorName = getCustomEntryFormForPropertyAndRange(prop, rangeUri);
+                editConfGeneratorName = getCustomEntryForm(prop);
             } else if( prop != null && prop.getCustomEntryForm() != null ){
                 //there is a custom form, great! let's use it.
                 editConfGeneratorName = prop.getCustomEntryForm();
@@ -247,25 +251,19 @@ public class EditRequestDispatchController extends FreemarkerHttpServlet {
         return editConfGeneratorName;
 	}
 
-	private String getCustomEntryFormForPropertyAndRange(Property prop, String rangeUri){
+	private String getCustomEntryForm(Property prop){
-	    String entryFormName = null;
+	    if (prop.getCustomEntryForm() == null) {
-	    // = ApplicationConfigurationOntologyUtils.getEntryForm(prop.getURI(), rangeUri);
+	        return DEFAULT_OBJ_FORM;
-	    if (entryFormName == null) {
-	        if (prop.getCustomEntryForm() != null) {
-	            return prop.getCustomEntryForm();
-	        } else {
-	            return DEFAULT_OBJ_FORM;
-	        }
 	    } else {
-	        prop.setCustomEntryForm(entryFormName);
+	        return prop.getCustomEntryForm();
-	        return entryFormName;
 	    }
 	}
 	
-	private Property getProperty(String predicateUri, VitroRequest vreq) {	   
+	private Property getProperty(String predicateUri, String domainUri, String rangeUri, VitroRequest vreq) {	   
 		Property p = null;
 		try{
-    		p = vreq.getWebappDaoFactory().getObjectPropertyDao().getObjectPropertyByURI(predicateUri);
+    		p = vreq.getWebappDaoFactory().getObjectPropertyDao().getObjectPropertyByURIs(
+    		        predicateUri, domainUri, rangeUri);
     		if(p == null) {
     			p = vreq.getWebappDaoFactory().getDataPropertyDao().getDataPropertyByURI(predicateUri);
     		}

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java

@@ -4,14 +4,17 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
 import java.io.IOException;
 import java.util.ArrayList;
-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.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -24,9 +27,10 @@ import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
-import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 
 /**  
 * Performs knowledge base updates to the abox to align with a new ontology version
@@ -34,10 +38,13 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
 */ 
 public class ABoxUpdater {
 
+    private final Log log = LogFactory.getLog(ABoxUpdater.class);
 	private OntModel oldTboxModel;
 	private OntModel newTboxModel;
-	private OntModel aboxModel;
+	private Dataset dataset;
+	private RDFService rdfService;
 	private OntModel newTBoxAnnotationsModel;
+	private TBoxUpdater tboxUpdater;
 	private ChangeLogger logger;  
 	private ChangeRecord record;
 	private OntClass OWL_THING = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createClass(OWL.Thing.getURI());
@@ -55,19 +62,19 @@ public class ABoxUpdater {
 	 *                         and the retractions model.
 	 *                    
 	 */
-	public ABoxUpdater(OntModel oldTboxModel,
+	public ABoxUpdater(UpdateSettings settings,
-			           OntModel newTboxModel,
-			           OntModel aboxModel,
-			           OntModel newAnnotationsModel,
 		               ChangeLogger logger,
 		               ChangeRecord record) {
 		
-		this.oldTboxModel = oldTboxModel;
+	    this.oldTboxModel = settings.getOldTBoxModel();
-		this.newTboxModel = newTboxModel;
+        this.newTboxModel = settings.getNewTBoxModel();
-		this.aboxModel = aboxModel;
+        RDFService rdfService = settings.getRDFService();
-		this.newTBoxAnnotationsModel = newAnnotationsModel;
+		this.dataset = new RDFServiceDataset(rdfService);
+		this.rdfService = rdfService;
+		this.newTBoxAnnotationsModel = settings.getNewTBoxAnnotationsModel();
 		this.logger = logger;
 		this.record = record;
+		this.tboxUpdater = new TBoxUpdater(settings, logger, record);
 	}
 	
 	/**
@@ -124,68 +131,75 @@ public class ABoxUpdater {
 	public void renameClass(AtomicOntologyChange change) throws IOException {
 		
 		//logger.log("Processing a class rename from: " + change.getSourceURI() + " to " + change.getDestinationURI());
-		aboxModel.enterCriticalSection(Lock.WRITE);
+	    
-		
+	    Iterator<String> graphIt = dataset.listNames();
-		try {
+	    while(graphIt.hasNext()) {
-			
+	        String graph = graphIt.next();
-	       Model additions = ModelFactory.createDefaultModel();
+	        if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
-	       Model retractions = ModelFactory.createDefaultModel();
+	            continue;
-	       
+	        }
-	       //TODO - look for these in the models and log error if not found
+	        Model aboxModel = dataset.getNamedModel(graph);
-		   Resource oldClass = ResourceFactory.createResource(change.getSourceURI());
+	        aboxModel.enterCriticalSection(Lock.WRITE);
-		   Resource newClass = ResourceFactory.createResource(change.getDestinationURI());	   
+    		try {
-		   
+    			
-		   // Change class references in the subjects of statements
+    	       Model additions = ModelFactory.createDefaultModel();
-		   
+    	       Model retractions = ModelFactory.createDefaultModel();
-		   // BJL 2010-04-09 : In future versions we need to keep track of
+    	       
-		   // the difference between true direct renamings and "use-insteads."
+    	       //TODO - look for these in the models and log error if not found
-		   // For now, the best behavior is to remove any remaining statements
+    		   Resource oldClass = ResourceFactory.createResource(change.getSourceURI());
-		   // where the old class is the subject, *unless* the statements
+    		   Resource newClass = ResourceFactory.createResource(change.getDestinationURI());	   
-		   // is part of the new annotations file (see comment below) or the
+    		   
-		   // predicate is vitro:autolinkedToTab.  In the latter case,
+    		   // Change class references in the subjects of statements
-		   // the autolinking annotation should be rewritten using the 
+    		   
-		   // new class name.
+    		   // BJL 2010-04-09 : In future versions we need to keep track of
-		   
+    		   // the difference between true direct renamings and "use-insteads."
-		   StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null);
+    		   // For now, the best behavior is to remove any remaining statements
-
+    		   // where the old class is the subject, *unless* the statements
-		   int removeCount = 0;
+    		   // is part of the new annotations file (see comment below) or the
-		   while (iter.hasNext()) {
+    		   // predicate is vitro:autolinkedToTab.  In the latter case,
-			   Statement oldStatement = iter.next();
+    		   // the autolinking annotation should be rewritten using the 
-			   removeCount++;
+    		   // new class name.
-			   retractions.add(oldStatement);
+    		   
-		   }
+    		   StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null);
-		   
+    
-		   //log summary of changes
+    		   int removeCount = 0;
-		   if (removeCount > 0) {
+    		   while (iter.hasNext()) {
-			   logger.log("Removed " + removeCount + " subject reference" + ((removeCount > 1) ? "s" : "") + " to the "  + oldClass.getURI() + " class");
+    			   Statement oldStatement = iter.next();
-		   }
+    			   removeCount++;
-
+    			   retractions.add(oldStatement);
-		   // Change class references in the objects of rdf:type statements
+    		   }
-		   iter = aboxModel.listStatements((Resource) null, RDF.type, oldClass);
+    		   
-
+    		   //log summary of changes
-		   int renameCount = 0;
+    		   if (removeCount > 0) {
-		   while (iter.hasNext()) {
+    			   logger.log("Removed " + removeCount + " subject reference" + ((removeCount > 1) ? "s" : "") + " to the "  + oldClass.getURI() + " class");
-			   renameCount++;
+    		   }
-			   Statement oldStatement = iter.next();
+    
-			   Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), RDF.type, newClass);
+    		   // Change class references in the objects of rdf:type statements
-			   retractions.add(oldStatement);
+    		   iter = aboxModel.listStatements((Resource) null, RDF.type, oldClass);
-			   additions.add(newStatement);
+    
-		   }
+    		   int renameCount = 0;
-		   
+    		   while (iter.hasNext()) {
-		   //log summary of changes
+    			   renameCount++;
-		   if (renameCount > 0) {
+    			   Statement oldStatement = iter.next();
-			   logger.log("Retyped " + renameCount + " individual" + ((renameCount > 1) ? "s" : "") + " from type "  + oldClass.getURI() + " to type " + newClass.getURI());
+    			   Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), RDF.type, newClass);
-		   }
+    			   retractions.add(oldStatement);
-		   
+    			   additions.add(newStatement);
-		   aboxModel.remove(retractions);
+    		   }
-		   record.recordRetractions(retractions);
+    		   
-		   aboxModel.add(additions);
+    		   //log summary of changes
-		   record.recordAdditions(additions);
+    		   if (renameCount > 0) {
-		   
+    			   logger.log("Retyped " + renameCount + " individual" + ((renameCount > 1) ? "s" : "") + " from type "  + oldClass.getURI() + " to type " + newClass.getURI());
-		} finally {
+    		   }
-			aboxModel.leaveCriticalSection();
+    		   
-		}
+    		   aboxModel.remove(retractions);
-		
+    		   record.recordRetractions(retractions);
+    		   aboxModel.add(additions);
+    		   record.recordAdditions(additions);
+    		   
+    		} finally {
+    			aboxModel.leaveCriticalSection();
+    		}
+	    }
 	}
 
 	/**
@@ -231,24 +245,26 @@ public class ABoxUpdater {
 
 			if (!parentOfAddedClass.equals(OWL.Thing)) {
 				
-				StmtIterator stmtIter = aboxModel.listStatements(null, RDF.type, parentOfAddedClass);
+			    Iterator<String> graphIt = dataset.listNames();
-				
+	            while(graphIt.hasNext()) {
-				int count = stmtIter.toList().size();
+	                String graph = graphIt.next();
-				if (count > 0) {
+	                if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
-					
+	                    continue;
-					String indList = "";
+	                }
-					while (stmtIter.hasNext()) {
+			        Model aboxModel = dataset.getNamedModel(graph);
-						Statement stmt = stmtIter.next();
+			            
-						indList += "\n\t" + stmt.getSubject().getURI(); 
+    				StmtIterator stmtIter = aboxModel.listStatements(null, RDF.type, parentOfAddedClass);
-					}
+    				
-					
+    				int count = stmtIter.toList().size();
+    					
 					if (count > 0) {
 						//TODO - take out the detailed logging after our internal testing is completed.
 				        logger.log("There " + ((count > 1) ? "are" : "is") + " " + count + " individual" + ((count > 1) ? "s" : "")  + " in the model that " + ((count > 1) ? "are" : "is") + " of type " + parentOfAddedClass.getURI() + "," +
 				        		    " and a new subclass of that class has been added: " + addedClass.getURI() + ". " +
 				        		    "Please review " + ((count > 1) ? "these" : "this") + " individual" + ((count > 1) ? "s" : "") + " to see whether " + ((count > 1) ? "they" : "it") + " should be of type: " +  addedClass.getURI() );
 					}
-				}				
+				
+	            }
 			}			
 		}
 	}
@@ -330,25 +346,33 @@ public class ABoxUpdater {
 		}
 		
 		// Remove instances of the deleted class
-		aboxModel.enterCriticalSection(Lock.WRITE);
+        Iterator<String> graphIt = dataset.listNames();
-	    try {
+        while(graphIt.hasNext()) {
-	       int count = 0;
+            String graph = graphIt.next();
-	       int refCount = 0;
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
-	       StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass);
+                continue;
-
+            }
-    	   while (iter.hasNext()) {
+            Model aboxModel = dataset.getNamedModel(graph);
-			   count++;
+    		aboxModel.enterCriticalSection(Lock.WRITE);
-			   Statement typeStmt = iter.next();   
+    	    try {
-			   refCount = deleteIndividual(typeStmt.getSubject());
+    	       int count = 0;
-		   }   
+    	       int refCount = 0;
-		   
+    	       StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass);
-		   if (count > 0) {
+    
-			   logger.log("Removed " + count + " individual" + (((count > 1) ? "s" : "") + " of type " + deletedClass.getURI()) + " (refs = " + refCount + ")");
+        	   while (iter.hasNext()) {
-		   }
+    			   count++;
-		   		   
+    			   Statement typeStmt = iter.next();   
-		} finally {
+    			   refCount = deleteIndividual(typeStmt.getSubject());
-			aboxModel.leaveCriticalSection();
+    		   }   
-		}
+    		   
+    		   if (count > 0) {
+    			   logger.log("Removed " + count + " individual" + (((count > 1) ? "s" : "") + " of type " + deletedClass.getURI()) + " (refs = " + refCount + ")");
+    		   }
+    		   		   
+    		} finally {
+    			aboxModel.leaveCriticalSection();
+    		}
+        }
 	}
 	
 	protected int deleteIndividual(Resource individual) throws IOException {
@@ -356,29 +380,37 @@ public class ABoxUpdater {
 	    Model retractions = ModelFactory.createDefaultModel();
 	    int refCount = 0;
 	    
-		aboxModel.enterCriticalSection(Lock.WRITE);
+        Iterator<String> graphIt = dataset.listNames();
-	    try {			   
+        while(graphIt.hasNext()) {
-		   StmtIterator iter = aboxModel.listStatements(individual, (Property) null, (RDFNode) null);
+            String graph = graphIt.next();
-			   
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
-		   while (iter.hasNext()) {
+                continue;
-			  Statement subjstmt = iter.next();
+            }
-			  retractions.add(subjstmt);
+            Model aboxModel = dataset.getNamedModel(graph);
-		   }
+    		aboxModel.enterCriticalSection(Lock.WRITE);
-			   
+    	    try {			   
-		   iter = aboxModel.listStatements((Resource) null, (Property) null, individual);
+    		   StmtIterator iter = aboxModel.listStatements(individual, (Property) null, (RDFNode) null);
-			   
+    			   
-		    while (iter.hasNext()) {
+    		   while (iter.hasNext()) {
-			    Statement objstmt = iter.next();
+    			  Statement subjstmt = iter.next();
-			    retractions.add(objstmt);
+    			  retractions.add(subjstmt);
-			    refCount++;
+    		   }
-			}
+    			   
-		   
+    		   iter = aboxModel.listStatements((Resource) null, (Property) null, individual);
-		   aboxModel.remove(retractions);
+    			   
-		   record.recordRetractions(retractions);		
+    		    while (iter.hasNext()) {
-		   
+    			    Statement objstmt = iter.next();
-		} finally {
+    			    retractions.add(objstmt);
-			aboxModel.leaveCriticalSection();
+    			    refCount++;
-		}
+    			}
+    		   
+    		   aboxModel.remove(retractions);
+    		   record.recordRetractions(retractions);		
+    		   
+    		} finally {
+    			aboxModel.leaveCriticalSection();
+    		}
+        }
 		
 		return refCount;
 	}
@@ -388,20 +420,33 @@ public class ABoxUpdater {
 		Iterator<AtomicOntologyChange> propItr = changes.iterator();
 		while(propItr.hasNext()){
 			AtomicOntologyChange propChangeObj = propItr.next();
-			switch (propChangeObj.getAtomicChangeType()){
+			log.debug("processing " + propChangeObj);
-			  case ADD: 
+			try {
-			   addProperty(propChangeObj);
+			    if (propChangeObj.getAtomicChangeType() == null) {
-			   break;
+			        log.error("Missing change type; skipping " + propChangeObj);
-			case DELETE: 
+			        continue;
-			   deleteProperty(propChangeObj);
+			    }
-			   break;
+    			switch (propChangeObj.getAtomicChangeType()){
-			case RENAME: 
+    			  case ADD: 
-			   renameProperty(propChangeObj);
+    			   log.debug("add");
-			   break;
+    			   addProperty(propChangeObj);
-			default: 
+    			   break;
-			   logger.logError("unexpected change type indicator: " + propChangeObj.getAtomicChangeType());
+    			case DELETE: 
-			   break;
+    			   log.debug("delete");
-		    }		
+    			   deleteProperty(propChangeObj);
+    			   break;
+    			case RENAME: 
+    			   log.debug("rename");
+    			   renameProperty(propChangeObj);
+    			   break;
+    			default: 
+    			   log.debug("unknown");
+    			   logger.logError("unexpected change type indicator: " + propChangeObj.getAtomicChangeType());
+    			   break;
+    		    }	
+			} catch (Exception e) {
+			    log.error(e,e);
+			}
 		}
 	}
 	
@@ -424,37 +469,45 @@ public class ABoxUpdater {
 		
 		if (inverseOfAddedProperty != null) {
 			Model additions = ModelFactory.createDefaultModel();
-			aboxModel.enterCriticalSection(Lock.WRITE);
+            Iterator<String> graphIt = dataset.listNames();
-			
+            while(graphIt.hasNext()) {
-			try {
+                String graph = graphIt.next();
-				StmtIterator iter = aboxModel.listStatements((Resource) null, inverseOfAddedProperty, (RDFNode) null);
+                if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
-		
+                    continue;
-				while (iter.hasNext()) {
+                }
-					
+                Model aboxModel = dataset.getNamedModel(graph);
-					Statement stmt = iter.next();
+    			aboxModel.enterCriticalSection(Lock.WRITE);
-					
+    			
-					if (stmt.getObject().isResource()) {
+    			try {
-					   Statement newStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), addedProperty, stmt.getSubject());
+    				StmtIterator iter = aboxModel.listStatements((Resource) null, inverseOfAddedProperty, (RDFNode) null);
-					   additions.add(newStmt);
+    		
-					} else {
+    				while (iter.hasNext()) {
-						logger.log("WARNING: expected the object of this statement to be a Resource but it is not. No inverse has been asserted: " + stmtString(stmt));
+    					
-					}
+    					Statement stmt = iter.next();
-				}
+    					
-				
+    					if (stmt.getObject().isResource()) {
-				aboxModel.add(additions);
+    					   Statement newStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), addedProperty, stmt.getSubject());
-				record.recordAdditions(additions);
+    					   additions.add(newStmt);
-				
+    					} else {
-				if (additions.size() > 0) {
+    						logger.log("WARNING: expected the object of this statement to be a Resource but it is not. No inverse has been asserted: " + stmtString(stmt));
-					logger.log("Added " + additions.size() + " statement" + 
+    					}
-							((additions.size() > 1) ? "s" : "") +
+    				}
-							" with predicate " + addedProperty.getURI() + 
+    				
-							" (as an inverse to existing  " + inverseOfAddedProperty.getURI() + 
+    				aboxModel.add(additions);
-							" statement" + ((additions.size() > 1) ? "s" : "") + ")");
+    				record.recordAdditions(additions);
-				}
+    				
-				
+    				if (additions.size() > 0) {
-			} finally {
+    					logger.log("Added " + additions.size() + " statement" + 
-				aboxModel.leaveCriticalSection();
+    							((additions.size() > 1) ? "s" : "") +
-			}
+    							" with predicate " + addedProperty.getURI() + 
+    							" (as an inverse to existing  " + inverseOfAddedProperty.getURI() + 
+    							" statement" + ((additions.size() > 1) ? "s" : "") + ")");
+    				}
+    				
+    			} finally {
+    				aboxModel.leaveCriticalSection();
+    			}
+            }
 		}
 	}
 	
@@ -492,33 +545,41 @@ public class ABoxUpdater {
 			}
 		}
 		
-		Model deletePropModel = ModelFactory.createDefaultModel();
+        Iterator<String> graphIt = dataset.listNames();
-		
+        while(graphIt.hasNext()) {
-		if (replacementProperty == null) {
+            String graph = graphIt.next();
-						
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
-			aboxModel.enterCriticalSection(Lock.WRITE);
+                continue;
-			try {
+            }
-				deletePropModel.add(aboxModel.listStatements((Resource) null, deletedProperty, (RDFNode) null));
+            Model aboxModel = dataset.getNamedModel(graph);
-				aboxModel.remove(deletePropModel);
+    		Model deletePropModel = ModelFactory.createDefaultModel();
-			} finally {
+    		
-				aboxModel.leaveCriticalSection();
+    		if (replacementProperty == null) {
-			}
+    						
-			record.recordRetractions(deletePropModel);
+    			aboxModel.enterCriticalSection(Lock.WRITE);
-			boolean plural = (deletePropModel.size() > 1);
+    			try {
-			if (deletePropModel.size() > 0) {
+    				deletePropModel.add(aboxModel.listStatements((Resource) null, deletedProperty, (RDFNode) null));
-				logger.log("Removed " + deletePropModel.size() + " statement" + (plural ? "s" : "") + " with predicate " + 
+    				aboxModel.remove(deletePropModel);
-						propObj.getSourceURI());
+    			} finally {
-			}
+    				aboxModel.leaveCriticalSection();
-		} else {
+    			}
-			AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes());
+    			record.recordRetractions(deletePropModel);
-			renameProperty(chg);
+    			boolean plural = (deletePropModel.size() > 1);
-		}		
+    			if (deletePropModel.size() > 0) {
+    				logger.log("Removed " + deletePropModel.size() + " statement" + (plural ? "s" : "") + " with predicate " + 
+    						propObj.getSourceURI());
+    			}
+    		} else {
+    			AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes());
+    			renameProperty(chg);
+    		}		
+        }
 		
 	}
 	
 	private void renameProperty(AtomicOntologyChange propObj) throws IOException {
 		
-		//logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
+		logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
 		
 		OntProperty oldProperty = oldTboxModel.getOntProperty(propObj.getSourceURI());
 		OntProperty newProperty = newTboxModel.getOntProperty(propObj.getDestinationURI());
@@ -533,35 +594,46 @@ public class ABoxUpdater {
 			return;
 		}
 		
-		Model renamePropAddModel = ModelFactory.createDefaultModel();
+        Iterator<String> graphIt = dataset.listNames();
-		Model renamePropRetractModel = 	ModelFactory.createDefaultModel();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
 		
-		aboxModel.enterCriticalSection(Lock.WRITE);
+    		Model renamePropAddModel = ModelFactory.createDefaultModel();
-		try {
+    		Model renamePropRetractModel = 	ModelFactory.createDefaultModel();
-			renamePropRetractModel.add(	aboxModel.listStatements(
+    		
-					(Resource) null, oldProperty, (RDFNode) null));
+    		aboxModel.enterCriticalSection(Lock.WRITE);
-			StmtIterator stmItr = renamePropRetractModel.listStatements();
+    		try {
-			while(stmItr.hasNext()) {
+    			renamePropRetractModel.add(	aboxModel.listStatements(
-				Statement tempStatement = stmItr.nextStatement();
+    					(Resource) null, oldProperty, (RDFNode) null));
-				renamePropAddModel.add( tempStatement.getSubject(),
+    			StmtIterator stmItr = renamePropRetractModel.listStatements();
-										newProperty,
+    			while(stmItr.hasNext()) {
-										tempStatement.getObject() );
+    				Statement tempStatement = stmItr.nextStatement();
-			}
+    				renamePropAddModel.add( tempStatement.getSubject(),
-			aboxModel.remove(renamePropRetractModel);
+    										newProperty,
-			aboxModel.add(renamePropAddModel);
+    										tempStatement.getObject() );
-		} finally {
+    			}
-			aboxModel.leaveCriticalSection();
+    			aboxModel.remove(renamePropRetractModel);
-		}
+    			aboxModel.add(renamePropAddModel);
-		
+    		} finally {
-		record.recordAdditions(renamePropAddModel);
+    			aboxModel.leaveCriticalSection();
-		record.recordRetractions(renamePropRetractModel);
+    		}
-		
+    		
-		if (renamePropRetractModel.size() > 0) {
+    		record.recordAdditions(renamePropAddModel);
-			logger.log("Changed " + renamePropRetractModel.size() + " statement" + 
+    		record.recordRetractions(renamePropRetractModel);
-					((renamePropRetractModel.size() > 1) ? "s" : "") +
+    		
-					" with predicate " + propObj.getSourceURI() + " to use " +
+    		if (renamePropRetractModel.size() > 0) {
-					propObj.getDestinationURI() + " instead");		
+    			logger.log("Changed " + renamePropRetractModel.size() + " statement" + 
-		}
+    					((renamePropRetractModel.size() > 1) ? "s" : "") +
+    					" with predicate " + propObj.getSourceURI() + " to use " +
+    					propObj.getDestinationURI() + " instead");		
+    		}
+        }
+        
+        tboxUpdater.renameProperty(propObj);
 	}
 	
 	public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/AtomicOntologyChange.java

@@ -30,6 +30,11 @@ public class AtomicOntologyChange {
 		this.notes = notes;
     }
 
+	@Override
+	public String toString() {
+	    return "Source: " + sourceURI + "; Destination: " + destinationURI +
+	            "; Type: " + atomicChangeType + "; Notes:" + notes;
+	}
 	
 	/**
 	 * Contains the URI of a class or property in the previous version of

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ChangeRecord.java

@@ -12,4 +12,6 @@ public interface ChangeRecord {
 	
 	public void writeChanges();
 	
+	public boolean hasRecordedChanges();
+	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java

@@ -11,6 +11,8 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -22,19 +24,16 @@ 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.Query;
+import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.Syntax;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.shared.Lock;
 
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
@@ -58,14 +57,13 @@ public class KnowledgeBaseUpdater {
 		this.record = new SimpleChangeRecord(settings.getAddedDataFile(), settings.getRemovedDataFile());
 	}
 	
-	public void update(ServletContext servletContext) throws IOException {	
+	public boolean update(ServletContext servletContext) throws IOException {	
 					
 		if (this.logger == null) {
 			this.logger = new SimpleChangeLogger(settings.getLogFile(),	settings.getErrorLogFile());
 		}
 			
 		long startTime = System.currentTimeMillis();
-        System.out.println("Migrating the knowledge base");
         log.info("Migrating the knowledge base");
         logger.log("Started knowledge base migration");
 		
@@ -73,7 +71,7 @@ public class KnowledgeBaseUpdater {
 		     performUpdate(servletContext);
 		} catch (Exception e) {
 			 logger.logError(e.getMessage());
-			 e.printStackTrace();
+			 log.error(e,e);
 		}
 
 		if (!logger.errorsWritten()) {
@@ -85,10 +83,9 @@ public class KnowledgeBaseUpdater {
 		logger.closeLogs();
 
 		long elapsedSecs = (System.currentTimeMillis() - startTime)/1000;		
-		System.out.println("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
 		log.info("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
 		
-		return;
+		return record.hasRecordedChanges();
 	}
 	
 	private void performUpdate(ServletContext servletContext) throws Exception {
@@ -98,136 +95,153 @@ public class KnowledgeBaseUpdater {
 		AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
 		
         //process the TBox before the ABox
-		log.info("\tupdating tbox annotations");
+		try {
-	    updateTBoxAnnotations();
+		    log.debug("\tupdating tbox annotations");
-
+	        updateTBoxAnnotations();
+		} catch (Exception e) {
+		    log.error(e,e);
+		}
+	    
 	    try {
     	    migrateMigrationMetadata(servletContext);
 		    logger.log("Migrated migration metadata");
 	    } catch (Exception e) {
-	    	log.debug("unable to migrate migration metadata " + e.getMessage());
+	    	log.error("unable to migrate migration metadata " + e.getMessage());
 	    }
-	    
+	        	
-		log.info("\tupdating the abox");
+    	log.info("performing SPARQL CONSTRUCT additions");
-    	updateABox(changes);
+    	performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
-	}
+    	
-		
+        log.info("performing SPARQL CONSTRUCT retractions");
-	private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
+        performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), settings.getRDFService(), RETRACT);
-		
+        
-		Model anonModel = performSparqlConstructs(sparqlConstructDir, readModel, true);
+        log.info("\tupdating the abox");
-		
+        updateABox(changes);
-		if (anonModel == null) {
+        
-			return;
+        log.info("performing post-processing SPARQL CONSTRUCT additions");
-		}
+        performSparqlConstructs(settings.getSparqlConstructAdditionsDir() + "/post/", 
-		
+                settings.getRDFService(), ADD);
-		writeModel.enterCriticalSection(Lock.WRITE);
+        
-		try {
+        log.info("performing post-processing SPARQL CONSTRUCT retractions");
-			JenaIngestUtils jiu = new JenaIngestUtils();
+        performSparqlConstructs(settings.getSparqlConstructDeletionsDir() + "/post/", 
-			Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", writeModel);
+                settings.getRDFService(), RETRACT);
-			Model actualAdditions = ModelFactory.createDefaultModel();
+        
-			StmtIterator stmtIt = additions.listStatements();
+
-			
-			while (stmtIt.hasNext()) {
-				Statement stmt = stmtIt.nextStatement();
-				if (!writeModel.contains(stmt)) {
-					actualAdditions.add(stmt);
-				}
-			}
-			
-			writeModel.add(actualAdditions);
-			record.recordAdditions(actualAdditions);
-		} finally {
-			writeModel.leaveCriticalSection();
-		}	
 	}
 	
-	private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
+    private static final boolean ADD = true;
-		
+    private static final boolean RETRACT = !ADD;
-		Model retractions = performSparqlConstructs(sparqlConstructDir, readModel, false);
-		
-		if (retractions == null) {
-			return;
-		}
-		
-		writeModel.enterCriticalSection(Lock.WRITE);
-		
-		try {
-			writeModel.remove(retractions);
-			record.recordRetractions(retractions);
-		} finally {
-			writeModel.leaveCriticalSection();
-		}
-		
-	}
 	
-	/**
+    /**
-	 * Performs a set of arbitrary SPARQL CONSTRUCT queries on the 
+     * Performs a set of arbitrary SPARQL CONSTRUCT queries on the 
-	 * data, for changes that cannot be expressed as simple property
+     * data, for changes that cannot be expressed as simple property
-	 * or class additions, deletions, or renamings.
+     * or class additions, deletions, or renamings.
-	 * Blank nodes created by the queries are given random URIs.
+     * Blank nodes created by the queries are given random URIs.
-	 * @param sparqlConstructDir
+     * @param sparqlConstructDir
-	 * @param aboxModel
+     * @param readModel
-	 */
+     * @param writeModel
-	private Model performSparqlConstructs(String sparqlConstructDir, 
+     * @param add (add = true; retract = false)
-			                              OntModel readModel,
+     */
-			                              boolean add)   throws IOException {
+    private void performSparqlConstructs(String sparqlConstructDir, 
-		
+            RDFService rdfService,
-		Model anonModel = ModelFactory.createDefaultModel();
+            boolean add)   throws IOException {
-		File sparqlConstructDirectory = new File(sparqlConstructDir);
+        Dataset dataset = new RDFServiceDataset(rdfService);
-		
+        File sparqlConstructDirectory = new File(sparqlConstructDir);
-		if (!sparqlConstructDirectory.isDirectory()) {
+        log.info("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
-			logger.logError(this.getClass().getName() + 
+        if (!sparqlConstructDirectory.isDirectory()) {
-					"performSparqlConstructs() expected to find a directory " +
+            String logMsg = this.getClass().getName() + 
-					" at " + sparqlConstructDir + ". Unable to execute " +
+                    "performSparqlConstructs() expected to find a directory " +
-					" SPARQL CONSTRUCTS.");
+                    " at " + sparqlConstructDir + ". Unable to execute " +
-			return null;
+                    " SPARQL CONSTRUCTS.";
-		}
+            logger.logError(logMsg);
-		
+            log.error(logMsg);
-		File[] sparqlFiles = sparqlConstructDirectory.listFiles();
+            return;
-		for (int i = 0; i < sparqlFiles.length; i ++) {
+        }
-			File sparqlFile = sparqlFiles[i];			
+        List<File> sparqlFiles = Arrays.asList(sparqlConstructDirectory.listFiles());
-			try {
+        Collections.sort(sparqlFiles); // queries may depend on being run in a certain order
-				BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
+        JenaIngestUtils jiu = new JenaIngestUtils();
-				StringBuffer fileContents = new StringBuffer();
+        for (File sparqlFile : sparqlFiles) {	
-				String ln;
+            if(sparqlFile.isDirectory()) {
-				
+                continue;
-				while ( (ln = reader.readLine()) != null) {
+            }
-					fileContents.append(ln).append('\n');
+            StringBuffer fileContents = new StringBuffer();
-				}
+            try {
-				
+                BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
-				try {
+                String ln;
-					log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFiles[i].getName());
+                while ( (ln = reader.readLine()) != null) {
-					Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
+                    fileContents.append(ln).append('\n');
-					readModel.enterCriticalSection(Lock.READ);
+                }
-					try {
+            } catch (FileNotFoundException fnfe) {
-						QueryExecution qe = QueryExecutionFactory.create(q,	readModel);
+                String logMsg = "WARNING: performSparqlConstructs() could not find " +
-						long numBefore = anonModel.size();
+                        " SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.";
-						qe.execConstruct(anonModel);
+                logger.log(logMsg);
-						long numAfter = anonModel.size();
+                log.info(logMsg);
-                        long num = numAfter - numBefore;
+                continue;
-                        
+            }   
-                        if (num > 0) {
+            Model anonModel = ModelFactory.createDefaultModel();
-						   logger.log((add ? "Added " : "Removed ") + num + 
+            try {
-								   " statement"  + ((num > 1) ? "s" : "") + 
+                log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
-								   " using the SPARQL construct query from file " + sparqlFiles[i].getParentFile().getName() + "/" + sparqlFiles[i].getName());
+                
+                anonModel = RDFServiceUtils.parseModel(
+                        rdfService.sparqlConstructQuery(fileContents.toString(), 
+                                RDFService.ModelSerializationFormat.NTRIPLE), 
+                                ModelSerializationFormat.NTRIPLE);
+
+                long num = anonModel.size();
+                if (num > 0) {
+                    String logMsg = (add ? "Added " : "Removed ") + num + 
+                            " statement"  + ((num > 1) ? "s" : "") + 
+                            " using the SPARQL construct query from file " + 
+                            sparqlFile.getParentFile().getName() +
+                            "/" + sparqlFile.getName();
+                    logger.log(logMsg);
+                    log.info(logMsg);
+                }
+        
+            } catch (Exception e) {
+                logger.logError(this.getClass().getName() + 
+                        ".performSparqlConstructs() unable to execute " +
+                        "query at " + sparqlFile + ". Error message is: " + e.getMessage());
+                log.error(e,e);
+            }
+        
+            if(!add) {
+                StmtIterator sit = anonModel.listStatements();
+                while (sit.hasNext()) {
+                    Statement stmt = sit.nextStatement();
+                    Iterator<String> graphIt = dataset.listNames();
+                    while(graphIt.hasNext()) {
+                        String graph = graphIt.next();
+                        if(!isUpdatableABoxGraph(graph)) {
+                            continue;
                         }
-                        qe.close();
+                        Model writeModel = dataset.getNamedModel(graph);
-					} finally {
+                        if (writeModel.contains(stmt)) {
-						readModel.leaveCriticalSection();
+                            writeModel.remove(stmt);
-					}
+                        }
-				} catch (Exception e) {
+                    }
-					logger.logError(this.getClass().getName() + 
+                }            
-							".performSparqlConstructs() unable to execute " +
+                record.recordRetractions(anonModel);
-							"query at " + sparqlFile + ". Error message is: " + e.getMessage());
+                //log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs");
-				}
+            } else {
-			} catch (FileNotFoundException fnfe) {
+                Model writeModel = dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL);
-				logger.log("WARNING: performSparqlConstructs() could not find " +
+                Model additions = jiu.renameBNodes(
-						   " SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.");
+                        anonModel, settings.getDefaultNamespace() + "n", writeModel);
-			}	
+                Model actualAdditions = ModelFactory.createDefaultModel();
-		}
+                StmtIterator stmtIt = additions.listStatements();      
-		
+                while (stmtIt.hasNext()) {
-        return anonModel;
+                    Statement stmt = stmtIt.nextStatement();
-	}
+                    if (!writeModel.contains(stmt)) {
+                        actualAdditions.add(stmt);
+                    }
+                }      
+                writeModel.add(actualAdditions);
+                //log.info("added " + actualAdditions.size() + " statements from SPARQL CONSTRUCTs");
+                record.recordAdditions(actualAdditions);
+            }
+            
+        }
+    }
 	
 	
 	private List<AtomicOntologyChange> getAtomicOntologyChanges() 
@@ -240,10 +254,8 @@ public class KnowledgeBaseUpdater {
 	private void updateABox(AtomicOntologyChangeLists changes) 
 			throws IOException {
 		
-		OntModel oldTBoxModel = settings.getOldTBoxModel();
+	
-		OntModel newTBoxModel = settings.getNewTBoxModel();
+		ABoxUpdater aboxUpdater = new ABoxUpdater(settings, logger, record);
-		OntModel ABoxModel = settings.getAssertionOntModelSelector().getABoxModel();
-		ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, ABoxModel,settings.getNewTBoxAnnotationsModel(), logger, record);
 		aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
 		aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
 	}
@@ -281,14 +293,18 @@ public class KnowledgeBaseUpdater {
 		rdfService.changeSetUpdate(removeChangeSet);	
 	}
 	
-	private void updateTBoxAnnotations() throws IOException {
+	private void updateTBoxAnnotations() {
-		
+		TBoxUpdater tboxUpdater = new TBoxUpdater(settings, logger, record);         
-		TBoxUpdater tboxUpdater = new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
+		try {
-		                                          settings.getNewTBoxAnnotationsModel(),
+		    tboxUpdater.modifyPropertyQualifications();
-                                                  settings.getAssertionOntModelSelector().getTBoxModel(), logger, record);
+		} catch (Exception e) {
-                                                  
+		    log.error("Unable to modify qualified property config file ", e);
-        tboxUpdater.updateDefaultAnnotationValues();
+		}
-        //tboxUpdater.updateAnnotationModel();
+		try {
+            tboxUpdater.updateDefaultAnnotationValues();
+		} catch (Exception e) {
+		    log.error("Unable to update default annotation values ", e);
+		}
 	}
 	
 	/**
@@ -296,7 +312,7 @@ public class KnowledgeBaseUpdater {
 	 * needs to be updated to conform to a new ontology version
 	 */
 	public boolean updateRequired(ServletContext servletContext) throws IOException {
-		boolean required = false;
+		boolean required = true;
 		
 		String sparqlQueryStr = loadSparqlQuery(settings.getAskUpdatedQueryFile());
 		if (sparqlQueryStr == null) {
@@ -338,7 +354,7 @@ public class KnowledgeBaseUpdater {
 		
 		File file = new File(filePath);	
 		if (!file.exists()) {
-			return null;
+			throw new RuntimeException("SPARQL file not found at " + filePath);
 		}
 		BufferedReader reader = new BufferedReader(new FileReader(file));
 		StringBuffer fileContents = new StringBuffer();
@@ -363,8 +379,10 @@ public class KnowledgeBaseUpdater {
 					" update to new ontology version: ", e);
 		}		
 	}
-		
+	
-
+	public static boolean isUpdatableABoxGraph(String graphName) {
+	    return (!graphName.contains("tbox") && !graphName.contains("filegraph"));
+	}
 
 	/**
 	 * A class that allows to access two different ontology change lists,
@@ -390,11 +408,13 @@ public class KnowledgeBaseUpdater {
 			while(listItr.hasNext()) {
 				AtomicOntologyChange changeObj = listItr.next();
 				if (changeObj.getSourceURI() != null){
-			
+			        log.debug("triaging " + changeObj);
 					if (oldTboxModel.getOntProperty(changeObj.getSourceURI()) != null){
 						 atomicPropertyChanges.add(changeObj);
+						 log.debug("added to property changes");
 					} else if (oldTboxModel.getOntClass(changeObj.getSourceURI()) != null) {
 						 atomicClassChanges.add(changeObj);
+						 log.debug("added to class changes");
 					} else if ("Prop".equals(changeObj.getNotes())) {
 						 atomicPropertyChanges.add(changeObj);
 					} else if ("Class".equals(changeObj.getNotes())) {
@@ -429,5 +449,6 @@ public class KnowledgeBaseUpdater {
 		public List<AtomicOntologyChange> getAtomicPropertyChanges() {
 			return atomicPropertyChanges;
 		}		
+		
 	}	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyChangeParser.java

@@ -9,6 +9,8 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.skife.csv.CSVReader;
 import org.skife.csv.SimpleReader;
 
@@ -23,6 +25,8 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
 
 public class OntologyChangeParser {
 
+    private final Log log = LogFactory.getLog(OntologyChangeParser.class);
+    
 	private ChangeLogger logger;
 	
 	public OntologyChangeParser(ChangeLogger logger) {
@@ -85,6 +89,8 @@ public class OntologyChangeParser {
 				}
 				
 				
+			    log.debug(changeObj);
+				
 				changeObjects.add(changeObj);
 					
 			}

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/SimpleChangeRecord.java

@@ -26,6 +26,9 @@ public class SimpleChangeRecord implements ChangeRecord {
 	private File additionsFile;
 	private File retractionsFile;
 	
+	private int additionsCount = 0;
+	private int retractionsCount = 0;
+	
 	public SimpleChangeRecord(
 			String additionsFile, String retractionsFile) {
 		this.additionsFile = new File(additionsFile);
@@ -46,11 +49,12 @@ public class SimpleChangeRecord implements ChangeRecord {
 	
 	public void recordAdditions(Model incrementalAdditions) {
 		additionsModel.add(incrementalAdditions);
-	
+	    additionsCount += incrementalAdditions.size();
 	}
 
 	public void recordRetractions(Model incrementalRetractions) {
 		retractionsModel.add(incrementalRetractions);
+		retractionsCount += incrementalRetractions.size();
 	}
 	
 	private void write(Model model, File file) {
@@ -71,5 +75,9 @@ public class SimpleChangeRecord implements ChangeRecord {
 			write(retractionsModel, retractionsFile);
 		}
 	}
+	
+	public boolean hasRecordedChanges() {
+	    return additionsCount > 0 || retractionsCount > 0;
+	}
 
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java

@@ -2,11 +2,22 @@
 
 package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.List;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
+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;
+import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -14,6 +25,7 @@ import com.hp.hpl.jena.rdf.model.NodeIterator;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
@@ -21,398 +33,542 @@ import com.hp.hpl.jena.vocabulary.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 /**  
-* Performs knowledge base updates to the tbox to align with a new ontology version
+ * Performs knowledge base updates to the tbox to align with a new ontology version
-*   
+ *   
-*/ 
+ */ 
 public class TBoxUpdater {
 
-	private OntModel oldTboxAnnotationsModel;
+    private static final Log log = LogFactory.getLog(TBoxUpdater.class);
-	private OntModel newTboxAnnotationsModel;
-	private OntModel siteModel;
-	private ChangeLogger logger;  
-	private ChangeRecord record;
-	private boolean detailLogs = false;
-	
-    private static final String classGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#ClassGroup";
-	private Resource classGroupClass = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource(classGroupURI);
-    private static final String inClassGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inClassGroup";
-	private Property inClassGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty(inClassGroupURI);
 
-	/**
+    private UpdateSettings settings;
-	 * 
+    private OntModel oldTboxAnnotationsModel;
-	 * Constructor 
+    private OntModel newTboxAnnotationsModel;
-	 *  
+    private OntModel siteModel;
-	 * @param   oldTboxAnnotationsModel - previous version of the annotations in the ontology
+    private ChangeLogger logger;  
-	 * @param   newTboxAnnotationsModel - new version of the annotations in the ontology
+    private ChangeRecord record;
-	 * @param   siteModel    - the knowledge base to be updated
+    private boolean detailLogs = false;
-	 * @param   logger       - for writing to the change log
+
-	 *                         and the error log.
+    private static final String classGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#ClassGroup";
-	 * @param   record       - for writing to the additions model 
+    private Resource classGroupClass = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource(classGroupURI);
-	 *                         and the retractions model.
+    private static final String inClassGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inClassGroup";
-	 *                    
+    private Property inClassGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty(inClassGroupURI);
-	 */
+
-	public TBoxUpdater(OntModel oldTboxAnnotationsModel,
+    /**
-			           OntModel newTboxAnnotationsModel,
+     * 
-			           OntModel siteModel,
+     * Constructor 
-		               ChangeLogger logger,
+     *  
-		               ChangeRecord record) {
+     * @param   oldTboxAnnotationsModel - previous version of the annotations in the ontology
-		
+     * @param   newTboxAnnotationsModel - new version of the annotations in the ontology
-		this.oldTboxAnnotationsModel = oldTboxAnnotationsModel;
+     * @param   siteModel    - the knowledge base to be updated
-		this.newTboxAnnotationsModel = newTboxAnnotationsModel;
+     * @param   logger       - for writing to the change log
-		this.siteModel = siteModel;
+     *                         and the error log.
-		this.logger = logger;
+     * @param   record       - for writing to the additions model 
-		this.record = record;
+     *                         and the retractions model.
-	}
+     *                    
-	
+     */
-	/**
+    public TBoxUpdater(UpdateSettings settings,
-	 * 
+            ChangeLogger logger,
-	 * Update a knowledge base to align with changes to vitro annotation property default 
+            ChangeRecord record) {
-	 * values in a new version of the ontology. The two versions of the ontology and the
+        this.settings = settings;
-	 * knowledge base to be updated are provided in the class constructor and are
+        this.oldTboxAnnotationsModel = settings.getOldTBoxAnnotationsModel();
-	 * referenced via class level variables. 
+        this.newTboxAnnotationsModel = settings.getNewTBoxAnnotationsModel();
-	 *                    
+        this.siteModel = settings.getAssertionOntModelSelector().getTBoxModel();
-	 * If the default value (i.e. the value that is provided in the vivo-core 
+        this.logger = logger;
-	 * annotations files) of a vitro annotation property has been changed for a vivo
+        this.record = record;
-	 * core class, and that default value has not been changed in the site knowledge
+    }
-	 * base, then update the value in the site knowledge base to be the new default.
+
-	 * Also, if a new vitro annotation property setting (i.e. either an existing 
+    /**
-	 * setting applied to an existing class where it wasn't applied before, or
+     * Update application ontology data for domain and range-qualified properties
-	 * an existing setting applied to a new class) has been applied to a vivo
+     * to use any applicable settings from obsolete subproperties
-	 * core class then copy that new property statement into the site model.
+     */
-	 * If a property setting for a class exists in the old ontology but
+    public void modifyPropertyQualifications() throws IOException {
-	 * not in the new one, then that statement will be removed from the
+ 
-	 * site knowledge base.
+    }
-	 *                    
+
-	 *  Writes to the change log file, the error log file, and the incremental change
+    private Model mergeConfigurations(Model oldConfig, Model newConfig) {
-	 *  knowledge base.                  
+        return null;
-	 *  
+    }
-	 *  Note: as specified, this method for now assumes that no new vitro annotation
+    
-	 *  properties have been introduced. This should be updated for future versions.
+    public void updateDefaultAnnotationValues() throws IOException {
-	 */
+        updateDefaultAnnotationValues(null);
-	public void updateDefaultAnnotationValues() throws IOException {
+    }
-				
+
-		siteModel.enterCriticalSection(Lock.WRITE);
+    /**
-		
+     * 
-		try {
+     * Update a knowledge base to align with changes to vitro annotation property default 
-			
+     * values in a new version of the ontology. The two versions of the ontology and the
-	       Model additions = ModelFactory.createDefaultModel();
+     * knowledge base to be updated are provided in the class constructor and are
-	       Model retractions = ModelFactory.createDefaultModel();
+     * referenced via class level variables. 
-		
+     *                    
-    	 //  Update defaults values for vitro annotation properties in the site model
+     * If the default value (i.e. the value that is provided in the vivo-core 
-         //  if the default has changed in the new version of the ontology AND if 
+     * annotations files) of a vitro annotation property has been changed for a vivo
-         //  the site hasn't overidden the previous default in their knowledge base.
+     * core class, and that default value has not been changed in the site knowledge
-    		    
+     * base, then update the value in the site knowledge base to be the new default.
-		  StmtIterator iter = oldTboxAnnotationsModel.listStatements();
+     * Also, if a new vitro annotation property setting (i.e. either an existing 
-		  		  		  
+     * setting applied to an existing class where it wasn't applied before, or
-		  while (iter.hasNext()) {
+     * an existing setting applied to a new class) has been applied to a vivo
-			  
+     * core class then copy that new property statement into the site model.
-			 Statement stmt = iter.next();
+     * If a property setting for a class exists in the old ontology but
-			 Resource subject = stmt.getSubject();
+     * not in the new one, then that statement will be removed from the
-			 Property predicate = stmt.getPredicate();
+     * site knowledge base.
-			 RDFNode oldObject = stmt.getObject();
+     *                    
-			 
+     *  Writes to the change log file, the error log file, and the incremental change
-			 if (! ( (RDFS.getURI().equals(predicate.getNameSpace())) || 
+     *  knowledge base.                  
-					 (VitroVocabulary.vitroURI.equals(predicate.getNameSpace())) 
+     *  
-					) ) {
+     *  Note: as specified, this method for now assumes that no new vitro annotation
-				 // this annotation updater is only concerned with properties
+     *  properties have been introduced. This should be updated for future versions.
-				 // such as rdfs:comment and properties in the vitro application
+     */
-				 // namespace
+    public void updateDefaultAnnotationValues(String subjectURI) throws IOException {
-				 continue;
+
-			 }
+        siteModel.enterCriticalSection(Lock.WRITE);
-			 			 
+
-			 NodeIterator newObjects = newTboxAnnotationsModel.listObjectsOfProperty(subject, predicate);
+        try {
-			 
+
-			 if ((newObjects == null) || (!newObjects.hasNext()) ) {
+            Model additions = ModelFactory.createDefaultModel();
-				 // first check to see if the site has a local value change
+            Model retractions = ModelFactory.createDefaultModel();
-				 // that should override the deletion
+
-				 List<RDFNode> siteObjects = siteModel.listObjectsOfProperty(subject, predicate).toList();
+            //  Update defaults values for vitro annotation properties in the site model
-				
+            //  if the default has changed in the new version of the ontology AND if 
-				 if (siteObjects.size() > 1) {
+            //  the site hasn't overidden the previous default in their knowledge base.
-					 /*
+
+            if(oldTboxAnnotationsModel == null) {
+                logger.log("oldTboxAnnotationModel is null; aborting update of annotation values");
+                return;
+            }
+            
+            Resource subj = (subjectURI == null) ? null : ResourceFactory.createResource(subjectURI);
+
+            StmtIterator iter = oldTboxAnnotationsModel.listStatements(subj, null, (RDFNode) null);
+
+            while (iter.hasNext()) {
+
+                Statement stmt = iter.next();
+                Resource subject = stmt.getSubject();
+                Property predicate = stmt.getPredicate();
+                RDFNode oldObject = stmt.getObject();
+
+                if (! ( (RDFS.getURI().equals(predicate.getNameSpace())) || 
+                        (VitroVocabulary.vitroURI.equals(predicate.getNameSpace())) 
+                        ) ) {
+                    // this annotation updater is only concerned with properties
+                    // such as rdfs:comment and properties in the vitro application
+                    // namespace
+                    continue;
+                }
+
+                NodeIterator newObjects = newTboxAnnotationsModel.listObjectsOfProperty(subject, predicate);
+
+                if ((newObjects == null) || (!newObjects.hasNext()) ) {
+                    // first check to see if the site has a local value change
+                    // that should override the deletion
+                    List<RDFNode> siteObjects = siteModel.listObjectsOfProperty(subject, predicate).toList();
+
+                    if (siteObjects.size() > 1) {
+                        /*
 					 logger.log("WARNING: found " + siteObjects.size() +
 					 		 " statements with subject = " + subject.getURI() + 
 							 " and property = " + predicate.getURI() +
 							 " in the site database (maximum of one is expected)");
-					 */
+                         */
-				 }
+                    }
-				 
+
-				 if (siteObjects.size() > 0) {
+                    if (siteObjects.size() > 0) {
-					 RDFNode siteNode = siteObjects.get(0);
+                        RDFNode siteNode = siteObjects.get(0);
-					 if (siteNode.equals(oldObject)) {
+                        if (siteNode.equals(oldObject)) {
-						 retractions.add(siteModel.listStatements(subject, predicate, (RDFNode) null));		 
+                            retractions.add(siteModel.listStatements(subject, predicate, (RDFNode) null));		 
-					 }
+                        }
-				 }
+                    }
-				 
+
-				 continue;				 			 
+                    continue;				 			 
-			 }
+                }
-			
+
-			 RDFNode newObject = newObjects.next();
+                RDFNode newObject = newObjects.next();
-			 
+
-			 int i = 1;
+                int i = 1;
-			 while (newObjects.hasNext()) {
+                while (newObjects.hasNext()) {
-                 i++;
+                    i++;
-                 newObjects.next();
+                    newObjects.next();
-             } 
+                } 
-			 
+
-			 if (i > 1) {
+                if (i > 1) {
-				 /*
+                    /*
 				 logger.log("WARNING: found " + i +
 						 " statements with subject = " + subject.getURI() + 
 						 " and property = " + predicate.getURI() +
 						 " in the new version of the annotations ontology (maximum of one is expected)");
-				 */		 
+                     */		 
-				 continue; 
+                    continue; 
-			 }
+                }
-			 
-			 // If a subject-property pair occurs in the old annotation TBox and the new annotations 
-			 // TBox, but not in the site model, then it is considered an erroneous deletion and
-			 // the value from the new TBox is added into the site model.
-			 // sjm: 7-16-2010. We want this here now to add back in annotations mistakenly dropped
-			 // in the .9 to 1.0 migration, but I'm not sure we would want this here permanently.
-			 // Shouldn't a site be allowed to delete annotations if they want to?
-			 
-			 NodeIterator siteObjects = siteModel.listObjectsOfProperty(subject,predicate);
-			 
-			 if (siteObjects == null || !siteObjects.hasNext()) {
-	        	    try {
-	    				additions.add(subject, predicate, newObject);
-	    			
-						if (detailLogs) {
-							   logger.log( "adding Statement: subject = " + subject.getURI() +
-								           " property = " + predicate.getURI() +
-				                           " object = " + (newObject.isLiteral() ?  ((Literal)newObject).getLexicalForm() 
-				                		                                          : ((Resource)newObject).getURI()));	
-							}
-					} catch (Exception e) {
-						logger.logError("Error trying to add statement with property " + predicate.getURI() +
-								" of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
-					}				 
-				 
-				   continue;
-			 }
-			 
-			 			 			 
-			 if (!newObject.equals(oldObject)) {
 
-				 RDFNode siteObject = siteObjects.next();
+                // If a subject-property pair occurs in the old annotation TBox and the new annotations 
+                // TBox, but not in the site model, then it is considered an erroneous deletion and
+                // the value from the new TBox is added into the site model.
+                // sjm: 7-16-2010. We want this here now to add back in annotations mistakenly dropped
+                // in the .9 to 1.0 migration, but I'm not sure we would want this here permanently.
+                // Shouldn't a site be allowed to delete annotations if they want to?
 
-		         i = 1;
+                NodeIterator siteObjects = siteModel.listObjectsOfProperty(subject,predicate);
-				 while (siteObjects.hasNext()) {
-					 i++; 
-					 siteObjects.next();
-				 } 
 
-				 if (i > 1) {
+                if (siteObjects == null || !siteObjects.hasNext()) {
-					 /*
+                    try {
+                        additions.add(subject, predicate, newObject);
+
+                        if (detailLogs) {
+                            logger.log( "adding Statement: subject = " + subject.getURI() +
+                                    " property = " + predicate.getURI() +
+                                    " object = " + (newObject.isLiteral() ?  ((Literal)newObject).getLexicalForm() 
+                                            : ((Resource)newObject).getURI()));	
+                        }
+                    } catch (Exception e) {
+                        logger.logError("Error trying to add statement with property " + predicate.getURI() +
+                                " of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
+                    }				 
+
+                    continue;
+                }
+
+
+                if (!newObject.equals(oldObject)) {
+
+                    RDFNode siteObject = siteObjects.next();
+
+                    i = 1;
+                    while (siteObjects.hasNext()) {
+                        i++; 
+                        siteObjects.next();
+                    } 
+
+                    if (i > 1) {
+                        /*
 					 logger.log("WARNING: found " + i +
 							 " statements with subject = " + subject.getURI() + 
 							 " and property = " + predicate.getURI() +
 							 " in the site annotations model (maximum of one is expected) "); 
-					 */
+                         */
-					 continue; 
+                        continue; 
-				 }
+                    }
-				 	 
-				 if (siteObject.equals(oldObject)) {
-	        	    try {
-	        	    	StmtIterator it = siteModel.listStatements(subject, predicate, (RDFNode)null);
-	        	    	while (it.hasNext()) {
-	        	    	  retractions.add(it.next());	
-	        	    	}
-					} catch (Exception e) {
-						logger.logError("Error removing statement for subject = " + subject.getURI() + 
-							            "and property = " + predicate.getURI() +
-							            "from the knowledge base:\n" + e.getMessage());
-					}
 
-	        	    try {
+                    if (siteObject.equals(oldObject)) {
-	    				additions.add(subject, predicate, newObject);
+                        try {
-	    				
+                            StmtIterator it = siteModel.listStatements(subject, predicate, (RDFNode)null);
-	    				if (detailLogs) {
+                            while (it.hasNext()) {
-						   logger.log("Changed the value of property "  + predicate.getURI() +
+                                retractions.add(it.next());	
-								" of subject = " + subject.getURI() + 
+                            }
-								" from " +
+                        } catch (Exception e) {
-								 (oldObject.isResource() ? ((Resource)oldObject).getURI() : ((Literal)oldObject).getLexicalForm()) +								
+                            logger.logError("Error removing statement for subject = " + subject.getURI() + 
-								" to " + 
+                                    "and property = " + predicate.getURI() +
-								 (newObject.isResource() ? ((Resource)newObject).getURI() : ((Literal)newObject).getLexicalForm()) +
+                                    "from the knowledge base:\n" + e.getMessage());
-								 " in the knowledge base:\n");
+                        }
-	    				}
-					} catch (Exception e) {
-						logger.logError("Error trying to change the value of property " + predicate.getURI() +
-								" of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
-					}
-				 }
-			 }		  
-		   }
-		     
-		   Model actualAdditions = additions.difference(retractions);
-		   siteModel.add(actualAdditions);
-		   record.recordAdditions(actualAdditions);
-		   Model actualRetractions = retractions.difference(additions);
-		   siteModel.remove(actualRetractions);
-		   record.recordRetractions(actualRetractions);
-		
-		   long numAdded = actualAdditions.size();
-		   long numRemoved = actualRetractions.size();
-		   
-		   // log summary of changes
-		   if (numAdded > 0) {
-	           logger.log("Updated the default vitro annotation value for " + 
-	        		   numAdded + " statements in the knowledge base");
-		   }
-		   
-           if (numRemoved > 0) {
-	           logger.log("Removed " + numRemoved +
-	        		      " outdated vitro annotation property setting" + ((numRemoved > 1) ? "s" : "") + " from the knowledge base");
-           }
-           
-		    //	   Copy annotation property settings that were introduced in the new ontology
-		    //     into the site model.
-		    //		  
 
-			Model newAnnotationSettings = newTboxAnnotationsModel.difference(oldTboxAnnotationsModel);
+                        try {
-			Model newAnnotationSettingsToAdd = ModelFactory.createDefaultModel();
+                            additions.add(subject, predicate, newObject);
-			StmtIterator newStmtIt = newAnnotationSettings.listStatements();
-			while (newStmtIt.hasNext()) {
-				Statement stmt = newStmtIt.next();
-				if (!siteModel.contains(stmt)) {
-					newAnnotationSettingsToAdd.add(stmt);
-				
-					if (detailLogs) {
-					   logger.log( "adding Statement: subject = " + stmt.getSubject().getURI() +
-						           " property = " + stmt.getPredicate().getURI() +
-		                           " object = " + (stmt.getObject().isLiteral() ?  ((Literal)stmt.getObject()).getLexicalForm() 
-		                		                                          : ((Resource)stmt.getObject()).getURI()));	
-					}
-				}
-			}
-			
-			siteModel.add(newAnnotationSettingsToAdd);
-			record.recordAdditions(newAnnotationSettingsToAdd);
-            
-			// log the additions - summary
-			if (newAnnotationSettingsToAdd.size() > 0) {
-				boolean plural = (newAnnotationSettingsToAdd.size() > 1);
-	            logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property setting" + (plural ? "s" : "") + " to the knowledge base. This includes only " +
-	                         "existing annotation properties applied to existing classes where they weren't applied before, or existing " +
-	                         "properties applied to new classes.");
-			}
-		   
-	} finally {
-		siteModel.leaveCriticalSection();
-	}
-}
-	
-/**
- * 
- * Update a knowledge base to align with changes to the vitro annotation model  
- * in a new version of the ontology. The two versions of the ontology and the
- * knowledge base to be updated are provided in the class constructor and are
- * referenced via class level variables. 
- *                    
- * Currently, this method only handles deletions of a ClassGroup
- *                    
- *  Writes to the change log file, the error log file, and the incremental change
- *  knowledge base.                  
- *  
- */	
-public void updateAnnotationModel() throws IOException {
-		
-	   // for each ClassGroup in the old vitro annotations model: if it is not in 
-	   // the new vitro annotations model and the site has no classes asserted to 
-	   // be in that class group then delete it.
-	   
-	   removeObsoleteAnnotations();
-	   
-	   siteModel.enterCriticalSection(Lock.WRITE);
-	   
-	   try {	
-		    Model retractions = ModelFactory.createDefaultModel();
-		    
-			StmtIterator iter = oldTboxAnnotationsModel.listStatements((Resource) null, RDF.type, classGroupClass);
-	  	
-			while (iter.hasNext()) {  
-			  Statement stmt = iter.next();
-						  
-			  if (!newTboxAnnotationsModel.contains(stmt) && !usesGroup(siteModel, stmt.getSubject())) {
-				  long pre = retractions.size();
-				  retractions.add(siteModel.listStatements(stmt.getSubject(),(Property) null,(RDFNode)null));
-				  long post = retractions.size();
-				  if ((post - pre) > 0) {
-				     logger.log("Removed the " + stmt.getSubject().getURI() + " ClassGroup from the annotations model");
-				  }  
-			  }
-			}
-	    	
-			if (retractions.size() > 0) {
-			   siteModel.remove(retractions);
-			   record.recordRetractions(retractions);
-		    }   
-		        
-		} finally {
-			siteModel.leaveCriticalSection();
-		}
 
-	   // If we were going to handle add, this is the logic:
+                            if (detailLogs) {
-	   // for each ClassGroup in new old vitro annotations model: if it is not in 
+                                logger.log("Changed the value of property "  + predicate.getURI() +
-	   // the old vitro annotations and it is not in the site model, then 
+                                        " of subject = " + subject.getURI() + 
-	   // add it.
+                                        " from " +
-	   
+                                        (oldObject.isResource() ? ((Resource)oldObject).getURI() : ((Literal)oldObject).getLexicalForm()) +								
-}
+                                        " to " + 
+                                        (newObject.isResource() ? ((Resource)newObject).getURI() : ((Literal)newObject).getLexicalForm()) +
+                                        " in the knowledge base:\n");
+                            }
+                        } catch (Exception e) {
+                            logger.logError("Error trying to change the value of property " + predicate.getURI() +
+                                    " of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
+                        }
+                    }
+                }		  
+            }
 
-public boolean usesGroup(Model model, Resource theClassGroup) throws IOException {
+            Model actualAdditions = additions.difference(retractions);
-	   
+            siteModel.add(actualAdditions);
-   model.enterCriticalSection(Lock.READ);
+            record.recordAdditions(actualAdditions);
-     
+            Model actualRetractions = retractions.difference(additions);
-   try {	   
+            siteModel.remove(actualRetractions);
-	   return (model.contains((Resource) null, inClassGroupProp, theClassGroup) ? true : false);
+            record.recordRetractions(actualRetractions);
-   } finally {
-	   model.leaveCriticalSection();
-   }
-}
 
-public void removeObsoleteAnnotations() throws IOException {
+            long numAdded = actualAdditions.size();
-		
+            long numRemoved = actualRetractions.size();
-	Resource subj1 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology/florida#StatewideGoalAndFocusArea");
+
-	Resource obj1 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroClassGrouptopics");
+            // log summary of changes
-	
+            if (numAdded > 0) {
-	Property subj2 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vivoweb.org/ontology/florida#divisionOfSponsoredResearchNumber");
+                logger.log("Updated the default vitro annotation value for " + 
-	Resource obj2 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroPropertyGroupidentifiers");
+                        numAdded + " statements in the knowledge base");
-	
+            }
-	Property subj3 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vivoweb.org/ontology/florida#statewideGoalAndFocusArea");
+
-	Resource obj3 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroPropertyGroupoutreach");
+            if (numRemoved > 0) {
-	
+                logger.log("Removed " + numRemoved +
-	Property inPropertyGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inPropertyGroup");
+                        " outdated vitro annotation property setting" + ((numRemoved > 1) ? "s" : "") + " from the knowledge base");
-	   
+            }
-    siteModel.enterCriticalSection(Lock.WRITE);
+
-   
+            //	   Copy annotation property settings that were introduced in the new ontology
-    try {	
+            //     into the site model.
-	    Model retractions = ModelFactory.createDefaultModel();
+            //		  
-	    
+
-        if (siteModel.contains(subj1, inClassGroupProp, obj1) ) {
+            Model newAnnotationSettings = newTboxAnnotationsModel.difference(oldTboxAnnotationsModel);
-        	retractions.add(subj1, inClassGroupProp, obj1);
+            Model newAnnotationSettingsToAdd = ModelFactory.createDefaultModel();
-        	logger.log("Removed statement " + ABoxUpdater.stmtString(subj1, inClassGroupProp, obj1) + " from the knowledge base (assumed to be obsolete)");
+            StmtIterator newStmtIt = newAnnotationSettings.listStatements();
+            while (newStmtIt.hasNext()) {
+                Statement stmt = newStmtIt.next();
+                if (!siteModel.contains(stmt)) {
+                    newAnnotationSettingsToAdd.add(stmt);
+
+                    if (detailLogs) {
+                        logger.log( "adding Statement: subject = " + stmt.getSubject().getURI() +
+                                " property = " + stmt.getPredicate().getURI() +
+                                " object = " + (stmt.getObject().isLiteral() ?  ((Literal)stmt.getObject()).getLexicalForm() 
+                                        : ((Resource)stmt.getObject()).getURI()));	
+                    }
+                }
+            }
+
+            siteModel.add(newAnnotationSettingsToAdd);
+            record.recordAdditions(newAnnotationSettingsToAdd);
+
+            // log the additions - summary
+            if (newAnnotationSettingsToAdd.size() > 0) {
+                boolean plural = (newAnnotationSettingsToAdd.size() > 1);
+                logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property setting" + (plural ? "s" : "") + " to the knowledge base. This includes only " +
+                        "existing annotation properties applied to existing classes where they weren't applied before, or existing " +
+                        "properties applied to new classes.");
+            }
+
+        } finally {
+            siteModel.leaveCriticalSection();
+        }
+    }
+
+    /**
+     * 
+     * Update a knowledge base to align with changes to the vitro annotation model  
+     * in a new version of the ontology. The two versions of the ontology and the
+     * knowledge base to be updated are provided in the class constructor and are
+     * referenced via class level variables. 
+     *                    
+     * Currently, this method only handles deletions of a ClassGroup
+     *                    
+     *  Writes to the change log file, the error log file, and the incremental change
+     *  knowledge base.                  
+     *  
+     */	
+    public void updateAnnotationModel() throws IOException {
+
+        // for each ClassGroup in the old vitro annotations model: if it is not in 
+        // the new vitro annotations model and the site has no classes asserted to 
+        // be in that class group then delete it.
+
+        removeObsoleteAnnotations();
+
+        siteModel.enterCriticalSection(Lock.WRITE);
+
+        try {	
+            Model retractions = ModelFactory.createDefaultModel();
+
+            StmtIterator iter = oldTboxAnnotationsModel.listStatements((Resource) null, RDF.type, classGroupClass);
+
+            while (iter.hasNext()) {  
+                Statement stmt = iter.next();
+
+                if (!newTboxAnnotationsModel.contains(stmt) && !usesGroup(siteModel, stmt.getSubject())) {
+                    long pre = retractions.size();
+                    retractions.add(siteModel.listStatements(stmt.getSubject(),(Property) null,(RDFNode)null));
+                    long post = retractions.size();
+                    if ((post - pre) > 0) {
+                        logger.log("Removed the " + stmt.getSubject().getURI() + " ClassGroup from the annotations model");
+                    }  
+                }
+            }
+
+            if (retractions.size() > 0) {
+                siteModel.remove(retractions);
+                record.recordRetractions(retractions);
+            }   
+
+        } finally {
+            siteModel.leaveCriticalSection();
         }
 
-        if (siteModel.contains(subj2, inPropertyGroupProp, obj2) ) {
+        // If we were going to handle add, this is the logic:
-        	retractions.add(subj2, inPropertyGroupProp, obj2);
+        // for each ClassGroup in new old vitro annotations model: if it is not in 
-        	logger.log("Removed statement " + ABoxUpdater.stmtString(subj2, inPropertyGroupProp, obj2) + " from the knowledge base (assumed to be obsolete)");
+        // the old vitro annotations and it is not in the site model, then 
-        }
+        // add it.
 
-        if (siteModel.contains(subj3, inPropertyGroupProp, obj3) ) {
+    }
-        	retractions.add(subj3, inPropertyGroupProp, obj3);
+
-        	logger.log("Removed statement " + ABoxUpdater.stmtString(subj3, inPropertyGroupProp, obj3) + " from the knowledge base (assumed to be obsolete)");
+    public boolean usesGroup(Model model, Resource theClassGroup) throws IOException {
+
+        model.enterCriticalSection(Lock.READ);
+
+        try {	   
+            return (model.contains((Resource) null, inClassGroupProp, theClassGroup) ? true : false);
+        } finally {
+            model.leaveCriticalSection();
         }
-    	
+    }
-		if (retractions.size() > 0) {
+
-		   siteModel.remove(retractions);
+    public void removeObsoleteAnnotations() throws IOException {
-		   record.recordRetractions(retractions);
+
-	    }   
+        Resource subj1 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology/florida#StatewideGoalAndFocusArea");
-	        
+        Resource obj1 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroClassGrouptopics");
-	 } finally {
+
-		siteModel.leaveCriticalSection();
+        Property subj2 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vivoweb.org/ontology/florida#divisionOfSponsoredResearchNumber");
-	 }
+        Resource obj2 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroPropertyGroupidentifiers");
-}
+
+        Property subj3 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vivoweb.org/ontology/florida#statewideGoalAndFocusArea");
+        Resource obj3 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroPropertyGroupoutreach");
+
+        Property inPropertyGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inPropertyGroup");
+
+        siteModel.enterCriticalSection(Lock.WRITE);
+
+        try {	
+            Model retractions = ModelFactory.createDefaultModel();
+
+            if (siteModel.contains(subj1, inClassGroupProp, obj1) ) {
+                retractions.add(subj1, inClassGroupProp, obj1);
+                logger.log("Removed statement " + ABoxUpdater.stmtString(subj1, inClassGroupProp, obj1) + " from the knowledge base (assumed to be obsolete)");
+            }
+
+            if (siteModel.contains(subj2, inPropertyGroupProp, obj2) ) {
+                retractions.add(subj2, inPropertyGroupProp, obj2);
+                logger.log("Removed statement " + ABoxUpdater.stmtString(subj2, inPropertyGroupProp, obj2) + " from the knowledge base (assumed to be obsolete)");
+            }
+
+            if (siteModel.contains(subj3, inPropertyGroupProp, obj3) ) {
+                retractions.add(subj3, inPropertyGroupProp, obj3);
+                logger.log("Removed statement " + ABoxUpdater.stmtString(subj3, inPropertyGroupProp, obj3) + " from the knowledge base (assumed to be obsolete)");
+            }
+
+            if (retractions.size() > 0) {
+                siteModel.remove(retractions);
+                record.recordRetractions(retractions);
+            }   
+
+        } finally {
+            siteModel.leaveCriticalSection();
+        }
+    }
+    
+    public void renameProperty(AtomicOntologyChange changeObj) throws IOException {
+        Dataset dataset = new RDFServiceDataset(settings.getRDFService());
+        Model userAnnotationsModel = dataset.getNamedModel(
+                JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
+        if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) {
+            mergePropertyAnnotationsToPropertyConfig(changeObj, userAnnotationsModel);
+        }        
+        Resource renamedProperty = userAnnotationsModel.getResource(changeObj.getSourceURI());
+        userAnnotationsModel.removeAll(renamedProperty, null, (RDFNode) null);
+        userAnnotationsModel.removeAll(null, null, renamedProperty);
+    }
+    
+    private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj,
+            Model userAnnotationsModel) throws IOException {
+        String contextURI = VitroVocabulary.PROPERTY_CONFIG_DATA + changeObj.getNotes().substring(3);
+        String oldPropertyURI = changeObj.getSourceURI();
+        
+        Model oldAnnotationsModel = settings.getOldTBoxAnnotationsModel();
+        
+        String propertyAnnotationsQuery = 
+                "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                "CONSTRUCT { \n" +
+                "    <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
+                "    <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
+                "    <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
+                "    <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
+                "    <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                "    <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
+                "} WHERE { \n" +
+                "    { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
+                "    UNION { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
+                "} \n" ; 
+        
+        Model userChangesModel = construct(
+                propertyAnnotationsQuery, userAnnotationsModel).difference(
+                        construct(propertyAnnotationsQuery, oldAnnotationsModel));
+        
+        String addQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                          "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                          "CONSTRUCT { \n" +
+                          "    ?configuration config:propertyGroup ?group . \n" +
+                          "    ?configuration config:displayName ?label . \n" +
+                          "    ?configuration vitro:displayRankAnnot ?displayRank . \n" +
+                          "    ?configuration vitro:customEntryFormAnnot ?customForm . \n" +
+                          "    ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                          "    ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +                              
+                          "} WHERE { \n" +
+                          "    <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
+                          "} \n" ;
+        
+        String retractQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                "CONSTRUCT { \n" +
+                "    <" + oldPropertyURI + "> config:propertyGroup ?rgroup . \n" +
+                "    ?configuration config:displayName ?rlabel . \n" +
+                "    ?configuration vitro:displayRankAnnot ?rdisplayRank . \n" +
+                "    ?configuration vitro:customEntryFormAnnot ?rcustomForm . \n" +
+                "    ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel . \n" +
+                "    ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?rupdateLevel . \n " +                              
+                "} WHERE { \n" +
+                "    <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
+                "               ?configuration config:propertyGroup ?rgroup } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
+                "               ?configuration config:displayName ?rlabel } \n " +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
+                "               ?configuration vitro:displayRantAnnot ?rdisplayRank } \n " +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
+                "               ?configuration vitro:customEntryFormAnnot ?rcustomForm } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                "               ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
+                "               ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } " +
+                "} \n" ;
+        
+        Model configModel = ModelFactory.createDefaultModel();
+        String configFileName = settings.getQualifiedPropertyConfigFile();
+        File file = new File(configFileName);
+        FileInputStream fis = new FileInputStream(file);
+        configModel.read(fis, null, "N3");
+
+        Model union = ModelFactory.createUnion(configModel, 
+                userChangesModel);
+
+        Model additions = construct(addQuery, union);
+        Model retractions = construct(retractQuery, union);
+        
+        if (additions.size() > 0 || retractions.size() > 0) {
+            configModel.remove(retractions);
+            log.info("Removing " + retractions.size() + " statements from " + contextURI);
+            configModel.add(additions);
+            log.info("Adding " + additions.size() + " statements from " + contextURI);
+            FileOutputStream fos = new FileOutputStream(file);
+            configModel.write(fos, "N3");
+        }
+    }
+    
+    private Model construct(String queryStr, Model model) {    
+        Query query = QueryFactory.create(queryStr);
+        QueryExecution qe = QueryExecutionFactory.create(query, model);
+        try {
+            return qe.execConstruct();
+        } finally {
+            qe.close();
+        }
+    }
 
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/UpdateSettings.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 
 public class UpdateSettings {
 
@@ -20,6 +21,7 @@ public class UpdateSettings {
 	private String errorLogFile;
 	private String addedDataFile;
 	private String removedDataFile;
+	private String qualifiedPropertyConfigFile;
 	private String defaultNamespace;
 	private OntModelSelector assertionOntModelSelector;
 	private OntModelSelector inferenceOntModelSelector;
@@ -37,6 +39,8 @@ public class UpdateSettings {
 	private OntModel newDisplayModelFromFile;
 	private OntModel loadedAtStartupDisplayModel;
 	private OntModel oldDisplayModelVivoListViewConfig;
+	private RDFService rdfService;
+	
 	public String getDataDir() {
 		return dataDir;
 	}
@@ -118,7 +122,13 @@ public class UpdateSettings {
 	public void setRemovedDataFile(String removedDataFile) {
 		this.removedDataFile = removedDataFile;
 	}
-	public String getDefaultNamespace() {
+	public String getQualifiedPropertyConfigFile() {
+	    return qualifiedPropertyConfigFile;
+	}
+	public void setQualifiedPropertyConfigFile(String qualifiedPropertyConfigFile) {
+	    this.qualifiedPropertyConfigFile = qualifiedPropertyConfigFile;
+	}
+ 	public String getDefaultNamespace() {
 		return defaultNamespace;
 	}
 	public void setDefaultNamespace(String defaultNamespace) {
@@ -223,6 +233,13 @@ public class UpdateSettings {
 		return this.oldDisplayModelVivoListViewConfig;
 	}
 	
+	public RDFService getRDFService() {
+	    return this.rdfService;
+	}
+	
+	public void setRDFService(RDFService rdfService) {
+	    this.rdfService = rdfService;
+	}
 	
 	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java

@@ -6,13 +6,16 @@ import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
 import java.util.ArrayList;
-import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
+import java.util.concurrent.ConcurrentLinkedQueue;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.graph.Node;
 import com.hp.hpl.jena.graph.Triple;
 import com.hp.hpl.jena.query.DataSource;
 import com.hp.hpl.jena.query.Dataset;
@@ -21,11 +24,9 @@ import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.QueryParseException;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
 import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.query.Syntax;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.RDFNode;
@@ -129,6 +130,7 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
                                 Resource s2 = (Resource) n;
                                 // now run yet another describe query
                                 String smallerTree = makeDescribe(s2);
+                                log.debug(smallerTree);
                                 Query smallerTreeQuery = QueryFactory.create(smallerTree);
                                 QueryExecution qe3 = QueryExecutionFactory.create(
                                         smallerTreeQuery, tree);
@@ -172,13 +174,17 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
         
         StringBuffer queryBuff = new StringBuffer();
         queryBuff.append("CONSTRUCT { \n");
-        addStatementPatterns(stmtIt, queryBuff, !WHERE_CLAUSE);
+        List<Statement> stmts = stmtIt.toList();
+        stmts = sort(stmts);
+        addStatementPatterns(stmts, queryBuff, !WHERE_CLAUSE);
         queryBuff.append("} WHERE { \n");
         if (graphURI != null) {
             queryBuff.append("    GRAPH <" + graphURI + "> { \n");
         }
         stmtIt = model.listStatements();
-        addStatementPatterns(stmtIt, queryBuff, WHERE_CLAUSE);
+        stmts = stmtIt.toList();
+        stmts = sort(stmts);
+        addStatementPatterns(stmts, queryBuff, WHERE_CLAUSE);
         if (graphURI != null) {
             queryBuff.append("    } \n");
         }
@@ -208,11 +214,61 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
         }       
     }
     
+    private List<Statement> sort(List<Statement> stmts) {
+        List<Statement> output = new ArrayList<Statement>();
+        int originalSize = stmts.size();
+        List <Statement> remaining = stmts;
+        ConcurrentLinkedQueue<Resource> subjQueue = new ConcurrentLinkedQueue<Resource>();
+        for(Statement stmt : remaining) {
+            if(stmt.getSubject().isURIResource()) {
+                subjQueue.add(stmt.getSubject());
+                break;
+            }
+        }
+        if (subjQueue.isEmpty()) {
+            throw new RuntimeException("No named subject in statement patterns");
+        }
+        while(remaining.size() > 0) {
+            if(subjQueue.isEmpty()) {
+                subjQueue.add(remaining.get(0).getSubject());
+            }
+            while(!subjQueue.isEmpty()) {
+                Resource subj = subjQueue.poll();
+                List<Statement> temp = new ArrayList<Statement>();
+                for (Statement stmt : remaining) {
+                    if(stmt.getSubject().equals(subj)) {
+                        output.add(stmt);
+                        if (stmt.getObject().isResource()) {
+                            subjQueue.add((Resource) stmt.getObject()); 
+                        }
+                    } else {
+                        temp.add(stmt);
+                    }
+                }
+                remaining = temp;
+            }
+        }
+        if(output.size() != originalSize) {
+            throw new RuntimeException("original list size was " + originalSize + 
+                    " but sorted size is " + output.size());      
+        }
+        return output;
+    }
+    
+    private String getHexString(Node node) {
+        String label = node.getBlankNodeLabel().replaceAll("\\W", "").toUpperCase();
+        if (label.length() > 7) {
+            return label.substring(label.length() - 7);
+        } else {
+            return label;
+        }
+    }
+    
     private static final boolean WHERE_CLAUSE = true;
     
-    private void addStatementPatterns(StmtIterator stmtIt, StringBuffer patternBuff, boolean whereClause) {
+    private void addStatementPatterns(List<Statement> stmts, StringBuffer patternBuff, boolean whereClause) {
-        while(stmtIt.hasNext()) {
+        for(Statement stmt : stmts) {
-            Triple t = stmtIt.next().asTriple();
+            Triple t = stmt.asTriple();
             patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
             patternBuff.append(" ");
             patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java

@@ -9,6 +9,7 @@ import java.io.StringWriter;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.concurrent.ConcurrentLinkedQueue;
 
 import org.apache.commons.httpclient.HttpClient;
 import org.apache.commons.httpclient.MultiThreadedHttpConnectionManager;
@@ -715,7 +716,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
         if (graphURI != null) {
             queryBuff.append("    GRAPH <" + graphURI + "> { \n");
         }
-        addStatementPatterns(stmtIt, queryBuff, !WHERE_CLAUSE);
+        List<Statement> stmts = stmtIt.toList();
+        sort(stmts);
+        addStatementPatterns(stmts, queryBuff, !WHERE_CLAUSE);
         if (graphURI != null) {
             queryBuff.append("    } \n");
         }
@@ -724,7 +727,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
             queryBuff.append("    GRAPH <" + graphURI + "> { \n");
         }
         stmtIt = model.listStatements();
-        addStatementPatterns(stmtIt, queryBuff, WHERE_CLAUSE);
+        stmts = stmtIt.toList();
+        sort(stmts);
+        addStatementPatterns(stmts, queryBuff, WHERE_CLAUSE);
         if (graphURI != null) {
             queryBuff.append("    } \n");
         }
@@ -736,11 +741,53 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
         executeUpdate(queryBuff.toString());
     }
     
+    private List<Statement> sort(List<Statement> stmts) {
+        List<Statement> output = new ArrayList<Statement>();
+        int originalSize = stmts.size();
+        List <Statement> remaining = stmts;
+        ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource> subjQueue = 
+                new ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource>();
+        for(Statement stmt : remaining) {
+            if(stmt.getSubject().isURIResource()) {
+                subjQueue.add(stmt.getSubject());
+                break;
+            }
+        }
+        if (subjQueue.isEmpty()) {
+            throw new RuntimeException("No named subject in statement patterns");
+        }
+        while(remaining.size() > 0) {
+            if(subjQueue.isEmpty()) {
+                subjQueue.add(remaining.get(0).getSubject());
+            }
+            while(!subjQueue.isEmpty()) {
+                com.hp.hpl.jena.rdf.model.Resource subj = subjQueue.poll();
+                List<Statement> temp = new ArrayList<Statement>();
+                for (Statement stmt : remaining) {
+                    if(stmt.getSubject().equals(subj)) {
+                        output.add(stmt);
+                        if (stmt.getObject().isResource()) {
+                            subjQueue.add((com.hp.hpl.jena.rdf.model.Resource) stmt.getObject()); 
+                        }
+                    } else {
+                        temp.add(stmt);
+                    }
+                }
+                remaining = temp;
+            }
+        }
+        if(output.size() != originalSize) {
+            throw new RuntimeException("original list size was " + originalSize + 
+                    " but sorted size is " + output.size());      
+        }
+        return output;
+    }
+    
     private static final boolean WHERE_CLAUSE = true;
     
-    private void addStatementPatterns(StmtIterator stmtIt, StringBuffer patternBuff, boolean whereClause) {
+    private void addStatementPatterns(List<Statement> stmts, StringBuffer patternBuff, boolean whereClause) {
-        while(stmtIt.hasNext()) {
+        for(Statement stmt : stmts) {
-            Triple t = stmtIt.next().asTriple();
+            Triple t = stmt.asTriple();
             patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
             patternBuff.append(" ");
             patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java

@@ -251,18 +251,24 @@ public class SimpleReasoner extends StatementListener {
 				    return;
 				}
 			
-				OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
+				OntClass subject, object;
-				if (subject == null) {
+				tboxModel.enterCriticalSection(Lock.READ);
-					log.debug("didn't find subject class in the tbox: " 
+				try {
-                              + (stmt.getSubject()).getURI());
+    				subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
-					return;
+    				if (subject == null) {
-				}
+    					log.debug("didn't find subject class in the tbox: " 
-				
+                                  + (stmt.getSubject()).getURI());
-				OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); 
+    					return;
-				if (object == null) {
+    				}
-					log.debug("didn't find object class in the tbox: " 
+    				
-                              + ((Resource)stmt.getObject()).getURI());
+    				object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); 
-					return;
+    				if (object == null) {
+    					log.debug("didn't find object class in the tbox: " 
+                                  + ((Resource)stmt.getObject()).getURI());
+    					return;
+    				}
+				} finally {
+				    tboxModel.leaveCriticalSection();
 				}
 				
 				if (stmt.getPredicate().equals(RDFS.subClassOf)) {
@@ -1672,6 +1678,10 @@ public class SimpleReasoner extends StatementListener {
                                             typeURIs = getRemainingAssertedTypeURIs(stmt.getSubject());
                                         }
                                         removedABoxTypeAssertion(stmt, inferenceModel, typeURIs);
+                                    } else if (doSameAs && stmt.getPredicate().equals(OWL.sameAs)) {
+                                        removedABoxSameAsAssertion(stmt, inferenceModel);   
+                                    } else {
+                                        removedABoxAssertion(stmt, inferenceModel);
                                     }
                                     doPlugins(ModelUpdate.Operation.RETRACT,stmt);
                                 } catch (NullPointerException npe) {

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

@@ -1,85 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.servlet.setup;
-
-import java.io.InputStream;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Set;
-
-import javax.servlet.ServletContextEvent;
-import javax.servlet.ServletContextListener;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.assembler.Assembler;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Resource;
-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;
-
-/**
- * This is the beginning of a more sane and flexible model management system,
- * especially necessary for DataStaR.
- * Don't use it yet; it's going to change.
- * (That part is still insane, I know.)
- * @author bjl23
- */
-public class AssembleModelsSetup implements ServletContextListener {
-
-	private static final Log log = LogFactory.getLog(AssembleModelsSetup.class);
-	
-	private List<Model> assembledModels = new LinkedList<Model>();
-	
-	private String ASSEMBLERS_DIR_PATH = "/WEB-INF/assemblers/";
-	private Resource ASSEMBLER_OBJECT = ResourceFactory.createProperty("http://jena.hpl.hp.com/2005/11/Assembler#Object");
-	private String SYNTAX = "N3";
-	
-	public void contextInitialized(ServletContextEvent sce) {
-		OntModel jenaOntModel = ModelAccess.on(sce.getServletContext()).getBaseOntModel();
-		// read assemblers out of assemblers directory
-		Set pathSet = sce.getServletContext().getResourcePaths(ASSEMBLERS_DIR_PATH);
-		for (String path : (Set<String>)pathSet) {
-			InputStream assemblerInputStream = sce.getServletContext().getResourceAsStream(path);
-			Model assemblerModel = ModelFactory.createDefaultModel();
-			try {
-				assemblerModel.read(assemblerInputStream, null, SYNTAX);
-				ExtendedIterator assemblerIt = assemblerModel.listResourcesWithProperty(RDF.type,ASSEMBLER_OBJECT);
-				while (assemblerIt.hasNext()) {
-					Resource assemblerObj = (Resource) assemblerIt.next();
-					Model assembledModel = Assembler.general.openModel(assemblerObj);
-					/* special stuff here */
-					Model memModel = ModelFactory.createDefaultModel();
-					memModel.add(assembledModel);
-					memModel.register(new ModelSynchronizer(assembledModel));
-					/* end special stuff */
-					if (assembledModel != null) {
-						jenaOntModel.addSubModel(memModel);
-					}
-				}
-				if (assemblerIt != null) {
-					assemblerIt.close();
-				}
-			} catch (Exception e) {
-				log.error("Unable to use assembler at "+path);
-			}
-		}
-		System.out.println("ContextListener AssembleModelsSetup done");
-	}
-	
-	public void contextDestroyed(ServletContextEvent sce) {
-		for (Model model : assembledModels) {
-			if (model != null) {
-				model.close();
-			}
-		}
-	}
-
-}

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

@@ -56,7 +56,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
             OntModelSelector inferencesOms = ModelAccess.on(ctx).getInferenceOntModelSelector();
             OntModelSelector unionOms = ModelAccess.on(ctx).getUnionOntModelSelector();
 
-			WebappDaoFactoryJena wadf = (WebappDaoFactoryJena) ModelAccess.on(ctx).getWebappDaoFactory();
+			WebappDaoFactory wadf = ModelAccess.on(ctx).getWebappDaoFactory();
             
             if (!assertionsOms.getTBoxModel().getProfile().NAMESPACE().equals(OWL.NAMESPACE.getNameSpace())) {        
                 log.error("Not connecting Pellet reasoner - the TBox assertions model is not an OWL model");
@@ -75,28 +75,24 @@ public class SimpleReasonerSetup implements ServletContextListener {
             sce.getServletContext().setAttribute("pelletListener",pelletListener);
             sce.getServletContext().setAttribute("pelletOntModel", pelletListener.getPelletModel());
             
-            if (wadf != null) {
+            if (wadf instanceof WebappDaoFactoryJena) {
-                wadf.setPelletListener(pelletListener);
+                ((WebappDaoFactoryJena) wadf).setPelletListener(pelletListener);
             }
             
             log.info("Pellet reasoner connected for the TBox");
      
-           // set up simple reasoning for the ABox
+            // set up simple reasoning for the ABox
-                    
+                                
-            DataSource bds = JenaDataSourceSetupBase
-                                    .getApplicationDataSource(ctx);
-            String dbType = ConfigurationProperties.getBean(ctx).getProperty( // database type
-                    "VitroConnection.DataSource.dbtype","MySQL");
-            
             RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService();            
             Dataset dataset = new RDFServiceDataset(rdfService);
             
             Model rebuildModel = dataset.getNamedModel(JENA_INF_MODEL_REBUILD); 
-            Model scratchModel = dataset.getNamedModel(JENA_INF_MODEL_SCRATCHPAD); 
+            Model scratchModel = dataset.getNamedModel(JENA_INF_MODEL_SCRATCHPAD);
+            Model inferenceModel = dataset.getNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL);
 
             // the simple reasoner will register itself as a listener to the ABox assertions
             SimpleReasoner simpleReasoner = new SimpleReasoner(
-                    unionOms.getTBoxModel(), rdfService, inferencesOms.getABoxModel(), rebuildModel, scratchModel);
+                    unionOms.getTBoxModel(), rdfService, inferenceModel, rebuildModel, scratchModel);
             sce.getServletContext().setAttribute(SimpleReasoner.class.getName(),simpleReasoner);
             
             StartupStatus ss = StartupStatus.getBean(ctx);
@@ -114,19 +110,6 @@ public class SimpleReasonerSetup implements ServletContextListener {
             }
             simpleReasoner.setPluginList(pluginList);
             
-            
-            if (isRecomputeRequired(sce.getServletContext())) {   
-                log.info("ABox inference recompute required.");
-                waitForTBoxReasoning(pelletListener);  
-                if (JenaDataSourceSetupBase.isFirstStartup()) {
-                    simpleReasoner.recompute();
-                } else {
-                    log.info("starting ABox inference recompute in a separate thread.");
-                    new Thread(new ABoxRecomputer(simpleReasoner),"ABoxRecomputer").start();
-                }
-                
-            } 
-
             SimpleReasonerTBoxListener simpleReasonerTBoxListener = new SimpleReasonerTBoxListener(simpleReasoner);
             sce.getServletContext().setAttribute(SimpleReasonerTBoxListener.class.getName(),simpleReasonerTBoxListener);
             assertionsOms.getTBoxModel().register(simpleReasonerTBoxListener);
@@ -139,16 +122,21 @@ public class SimpleReasonerSetup implements ServletContextListener {
         }        
     }
     
-    private void waitForTBoxReasoning(PelletListener pelletListener) 
+    public static void waitForTBoxReasoning(ServletContextEvent sce) 
         throws InterruptedException {
-      int sleeps = 0;
+        PelletListener pelletListener = (PelletListener) sce.getServletContext().getAttribute("pelletListener");
-      while (sleeps < 1000 && pelletListener.isReasoning()) {
+        if (pelletListener == null) {
-          if ((sleeps % 10) == 0) { // print message at 10 second intervals
+            return ;
-              log.info("Waiting for initial TBox reasoning to complete");
+        }
-          }
+        int sleeps = 0;
-          Thread.sleep(1000);   
+        // sleep at least once to make sure the TBox reasoning gets started
-          sleeps++;
+        while ((0 == sleeps) || ((sleeps < 1000) && pelletListener.isReasoning())) {
-      }
+            if ((sleeps % 10) == 0) { // print message at 10 second intervals
+                log.info("Waiting for initial TBox reasoning to complete");
+            }
+            Thread.sleep(1000);   
+            sleeps++;
+        }
     }
     
     @Override
@@ -196,7 +184,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
         ctx.setAttribute(RECOMPUTE_REQUIRED_ATTR, true);
     }
     
-    private static boolean isRecomputeRequired(ServletContext ctx) {
+    public static boolean isRecomputeRequired(ServletContext ctx) {
         return (ctx.getAttribute(RECOMPUTE_REQUIRED_ATTR) != null);
     }
   
@@ -210,19 +198,6 @@ public class SimpleReasonerSetup implements ServletContextListener {
     private static boolean isMSTComputeRequired(ServletContext ctx) {
         return (ctx.getAttribute(MSTCOMPUTE_REQUIRED_ATTR) != null);
     }
-    
-    private class ABoxRecomputer implements Runnable {
-        
-        private SimpleReasoner simpleReasoner;
-        
-        public ABoxRecomputer(SimpleReasoner simpleReasoner) {
-            this.simpleReasoner = simpleReasoner;
-        }
-        
-        public void run() {
-            simpleReasoner.recompute();
-        }
-    }
         
     /**
      * Read the names of the plugin classes classes.

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

@@ -41,6 +41,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.UpdateSettings;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
+import edu.cornell.mannlib.vitro.webapp.reasoner.ABoxRecomputer;
+import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 /**
@@ -54,10 +57,11 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 	private final static Log log = LogFactory.getLog(UpdateKnowledgeBase.class);
 	
 	private static final String DATA_DIR = "/WEB-INF/ontologies/update/";
+	private static final String DIFF_FILE = DATA_DIR + "diff.tab.txt";
+	private static final String ASK_QUERY_FILE = DATA_DIR + "askUpdated.sparql";
+	private static final String SUCCESS_ASSERTIONS_FILE = DATA_DIR + "success.n3";
 	private static final String OLD_TBOX_MODEL_DIR = DATA_DIR + "oldVersion/";
-	private static final String NEW_TBOX_MODEL_DIR = "/WEB-INF/filegraph/tbox/";
 	private static final String OLD_TBOX_ANNOTATIONS_DIR = DATA_DIR + "oldAnnotations/";
-	private static final String NEW_TBOX_ANNOTATIONS_DIR = "/WEB-INF/ontologies/user/tbox/";
 	//For display model migration
 	private static final String OLD_DISPLAYMODEL_TBOX_PATH = DATA_DIR + "oldDisplayModel/displayTBOX.n3";
 	private static final String NEW_DISPLAYMODEL_TBOX_PATH = "/WEB-INF/ontologies/app/menuload/displayTBOX.n3";
@@ -72,78 +76,136 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		ServletContext ctx = sce.getServletContext();
 		StartupStatus ss = StartupStatus.getBean(ctx);
 
+        boolean migrationChangesMade = false;
+		
 		try {
 			UpdateSettings settings = new UpdateSettings();
 			putReportingPathsIntoSettings(ctx, settings);
+			putNonReportingPathsIntoSettings(ctx, settings);
 
+            SimpleReasonerSetup.waitForTBoxReasoning(sce); 
+			
 			WebappDaoFactory wadf = ModelAccess.on(ctx).getWebappDaoFactory();
 			settings.setDefaultNamespace(wadf.getDefaultNamespace());
 			settings.setAssertionOntModelSelector(ModelAccess.on(ctx).getBaseOntModelSelector());
 			settings.setInferenceOntModelSelector(ModelAccess.on(ctx).getInferenceOntModelSelector());
 			settings.setUnionOntModelSelector(ModelAccess.on(ctx).getUnionOntModelSelector());
+			
+		    ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
+		    Path homeDir = Paths.get(props.getProperty("vitro.home"));
+			settings.setDisplayModel(ModelAccess.on(ctx).getDisplayModel());
+			OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
+			settings.setOldTBoxModel(oldTBoxModel);
+			OntModel newTBoxModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "filegraph").toString());
+			settings.setNewTBoxModel(newTBoxModel);
+			OntModel oldTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_ANNOTATIONS_DIR));
+			settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
+			OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "firsttime").toString());
+			settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
+			settings.setRDFService(RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService());
+
 			boolean tryMigrateDisplay = true;
 			try {
-				settings.setDisplayModel(ModelAccess.on(ctx).getDisplayModel());
+			    //Display model tbox and display metadata 
-				OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
+			    //old display model tbox model
-				settings.setOldTBoxModel(oldTBoxModel);
+			    OntModel oldDisplayModelTboxModel = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_TBOX_PATH));
-				OntModel newTBoxModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_MODEL_DIR));
+			    settings.setOldDisplayModelTboxModel(oldDisplayModelTboxModel);
-				settings.setNewTBoxModel(newTBoxModel);
+			    //new display model tbox model
-				OntModel oldTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_ANNOTATIONS_DIR));
+			    OntModel newDisplayModelTboxModel = loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_TBOX_PATH));
-				settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
+			    settings.setNewDisplayModelTboxModel(newDisplayModelTboxModel);
-				OntModel newTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_ANNOTATIONS_DIR));
+			    //old display model display model metadata
-				settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
+			    OntModel oldDisplayModelDisplayMetadataModel = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_DISPLAYMETADATA_PATH));
-				//Display model tbox and display metadata 
+			    settings.setOldDisplayModelDisplayMetadataModel(oldDisplayModelDisplayMetadataModel);
-				//old display model tbox model
+			    //new display model display model metadata
-				OntModel oldDisplayModelTboxModel = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_TBOX_PATH));
+			    OntModel newDisplayModelDisplayMetadataModel = loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_DISPLAYMETADATA_PATH));
-				settings.setOldDisplayModelTboxModel(oldDisplayModelTboxModel);
+			    settings.setNewDisplayModelDisplayMetadataModel(newDisplayModelDisplayMetadataModel);
-				//new display model tbox model
+			    //Get new display model
-				OntModel newDisplayModelTboxModel = loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_TBOX_PATH));
+			    OntModel newDisplayModelFromFile = loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_PATH));
-				settings.setNewDisplayModelTboxModel(newDisplayModelTboxModel);
+			    settings.setNewDisplayModelFromFile(newDisplayModelFromFile);
-				//old display model display model metadata
+			    OntModel loadedAtStartupFiles = loadModelFromDirectory(ctx.getRealPath(LOADED_STARTUPT_DISPLAYMODEL_DIR));
-				OntModel oldDisplayModelDisplayMetadataModel = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_DISPLAYMETADATA_PATH));
+			    settings.setLoadedAtStartupDisplayModel(loadedAtStartupFiles);
-				settings.setOldDisplayModelDisplayMetadataModel(oldDisplayModelDisplayMetadataModel);
+			    OntModel oldDisplayModelVivoListView = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_VIVOLISTVIEW_PATH));
-				//new display model display model metadata
+			    settings.setVivoListViewConfigDisplayModel(oldDisplayModelVivoListView);
-				OntModel newDisplayModelDisplayMetadataModel = loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_DISPLAYMETADATA_PATH));
+			} catch (ModelFileNotFoundException e) {
-				settings.setNewDisplayModelDisplayMetadataModel(newDisplayModelDisplayMetadataModel);
+			    // expected if no display migration was intended
-				//Get new display model
+			    tryMigrateDisplay = false;
-				OntModel newDisplayModelFromFile = loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_PATH));
-				settings.setNewDisplayModelFromFile(newDisplayModelFromFile);
-				OntModel loadedAtStartupFiles = loadModelFromDirectory(ctx.getRealPath(LOADED_STARTUPT_DISPLAYMODEL_DIR));
-				settings.setLoadedAtStartupDisplayModel(loadedAtStartupFiles);
-				OntModel oldDisplayModelVivoListView = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_VIVOLISTVIEW_PATH));
-				settings.setVivoListViewConfigDisplayModel(oldDisplayModelVivoListView);
 			} catch (Exception e) {
-				log.info("unable to read display model migration files, display model not migrated. " + e.getMessage());
+			    log.info("Unable to read display model migration files. ", e);
-				tryMigrateDisplay = false;
+			    tryMigrateDisplay = false;
 			}
-				
+
-			try {		
+
-			   KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
+			KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
-			  
+			boolean requiredUpdate = ontologyUpdater.updateRequired(ctx);
-			   try {
+
-				  if (ontologyUpdater.updateRequired(ctx)) {
+			try {
-					  ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
+			    ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
-					  ontologyUpdater.update(ctx);
+			    log.info("Data migration required");
-					  if (tryMigrateDisplay) {
+			    migrationChangesMade = ontologyUpdater.update(ctx);
-						  try {
+			    if (tryMigrateDisplay) {
-						       migrateDisplayModel(settings);
+			        try {
-						       log.info("Migrated display model");
+			            migrateDisplayModel(settings);
-						  } catch (Exception e) {
+			            log.info("Migrated display model");
-							   log.warn("unable to successfully update display model: " + e.getMessage());
+			        } catch (Exception e) {
-						  }
+			            log.warn("unable to successfully update display model: " + e.getMessage());
-					  }
+			        }
-				  }
+			    }
-			   } catch (Exception ioe) {
+			    // reload the display model since the TBoxUpdater may have 
-					ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
+			    // modified it
-			   }	
+			    new ApplicationModelSetup().contextInitialized(sce);				  
-			} catch (Throwable t){
+			} catch (Exception ioe) {
-				ss.fatal(this, "Exception updating knowledge base for ontology changes: ", t);
+			    ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
-			}
+			}	
-		} catch (Throwable t) {
+
-			ss.fatal(this, "Exception updating knowledge base for ontology changes: ", t);
+		    SimpleReasoner simpleReasoner = (SimpleReasoner) sce.getServletContext()
+		            .getAttribute(SimpleReasoner.class.getName());
+		    if (simpleReasoner != null) {
+		        if ( (requiredUpdate && migrationChangesMade) 
+		                || JenaDataSourceSetupBase.isFirstStartup()) {
+		            log.info("ABox inference recompute required.");
+		            simpleReasoner.recompute();
+		        } else if (SimpleReasonerSetup.isRecomputeRequired(sce.getServletContext()) || migrationChangesMade) {
+		            log.info("starting ABox inference recompute in a separate thread.");
+		            new Thread(
+		                    new ABoxRecomputer(
+		                            simpleReasoner),"ABoxRecomputer").start();
+		        }
+		    }			
+			
+		} catch (Throwable t){
+		    ss.fatal(this, "Exception updating knowledge base for ontology changes: ", t);
 		}
+        
+
+		
 	}	
 
+	private class ABoxRecomputer implements Runnable {
+
+	    private SimpleReasoner simpleReasoner;
+
+	    public ABoxRecomputer(SimpleReasoner simpleReasoner) {
+	        this.simpleReasoner = simpleReasoner;
+	    }
+
+	    public void run() {
+	        simpleReasoner.recompute();
+	    }
+	}
+
+	
+	/**
+	 * Set the paths for the files that specify how to perform the update
+	 */
+	private void putNonReportingPathsIntoSettings(ServletContext ctx, UpdateSettings settings) {
+        settings.setAskUpdatedQueryFile(ctx.getRealPath(ASK_QUERY_FILE));
+        settings.setDiffFile(ctx.getRealPath(DIFF_FILE));
+        settings.setSparqlConstructAdditionsDir(ctx.getRealPath(DATA_DIR + "sparqlConstructs/additions"));
+        settings.setSparqlConstructDeletionsDir(ctx.getRealPath(DATA_DIR + "sparqlConstructs/deletions"));
+        settings.setSuccessAssertionsFile(ctx.getRealPath(SUCCESS_ASSERTIONS_FILE));
+        settings.setSuccessRDFFormat("N3");
+	}
+	
 	/**
 	 * Create the directories where we will report on the update. 
 	 * Put the paths for the directories and files into the settings object.
@@ -156,14 +218,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		settings.setDataDir(dataDir.toString());
 		StartupStatus.getBean(ctx).info(this, "Updating knowledge base: reports are in '" + dataDir + "'");
 
-		settings.setAskUpdatedQueryFile(dataDir.resolve("askUpdated.sparql").toString());
-		settings.setDiffFile(dataDir.resolve("diff.tab.txt").toString());
-		settings.setSuccessAssertionsFile(dataDir.resolve("success.n3").toString());
-		settings.setSuccessRDFFormat("N3");
-
-		settings.setSparqlConstructAdditionsDir(createDirectory(dataDir, "sparqlConstructs", "additions").toString());
-		settings.setSparqlConstructDeletionsDir(createDirectory(dataDir, "sparqlConstructs", "deletions").toString());
-		
 		Path changedDir = createDirectory(dataDir, "changedData");
 		settings.setAddedDataFile(changedDir.resolve("addedData.n3").toString());
 		settings.setRemovedDataFile(changedDir.resolve("removedData.n3").toString());
@@ -171,8 +225,19 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		Path logDir = createDirectory(dataDir, "logs");
 		settings.setLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate", "log")).toString());
 		settings.setErrorLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate.error", "log")).toString());
+		
+		Path qualifiedPropertyConfigFile = getFilePath(homeDir, "rdf", "display", "everytime", "PropertyConfig.n3");
+		settings.setQualifiedPropertyConfigFile(qualifiedPropertyConfigFile.toString());
 	}
 
+	private Path getFilePath(Path parent, String... children) throws IOException {
+        Path path = parent;
+        for (String child : children) {
+            path = path.resolve(child);
+        }
+        return path;	    
+	}
+	
 	private Path createDirectory(Path parent, String... children) throws IOException {
 		Path dir = parent;
 		for (String child : children) {

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/ApplicationConfigurationOntologyUtils.java

@@ -10,100 +10,119 @@ import javax.servlet.ServletContext;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 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.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess.ModelID;
+import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
 
 public class ApplicationConfigurationOntologyUtils {
 
     private static final Log log = LogFactory.getLog(ApplicationConfigurationOntologyUtils.class);
     
-    public static List<ObjectProperty> getAdditionalFauxSubpropertiesForList(List<ObjectProperty> propList, VitroRequest vreq) {
+    public static List<ObjectProperty> getAdditionalFauxSubpropertiesForList(List<ObjectProperty> propList, Individual subject, VitroRequest vreq) {
         ServletContext ctx = vreq.getSession().getServletContext();
 		Model displayModel = ModelAccess.on(ctx).getDisplayModel();
         Model tboxModel = ModelAccess.on(ctx).getOntModel(ModelID.UNION_TBOX);
-        return getAdditionalFauxSubpropertiesForList(propList, displayModel, tboxModel);
+        return getAdditionalFauxSubpropertiesForList(propList, subject, displayModel, tboxModel);
     }
     
+    public static List<ObjectProperty> getAdditionalFauxSubproperties(ObjectProperty prop, 
+                                                                         Individual subject,
+                                                                         Model tboxModel,
+                                                                         Model union) {
+
+        List<ObjectProperty> additionalProps = new ArrayList<ObjectProperty>();
+        String queryStr = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
+                "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
+                "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
+                "SELECT DISTINCT ?range ?domain ?property WHERE { \n" +
+                "    ?context config:configContextFor ?property . \n" +
+                "    ?context config:qualifiedBy ?range . \n" +
+                "    ?context config:hasConfiguration ?configuration . \n" +
+                "    ?configuration a config:ObjectPropertyDisplayConfig . \n" +
+                "    OPTIONAL { ?context config:qualifiedByDomain ?domain } \n" +
+                "}"; 
+      
+        if(prop != null) {
+            log.debug("Checking " + prop.getURI() + " for additional properties");
+            queryStr = queryStr.replaceAll("For \\?property", "For <" + prop.getURI() + ">");
+        }
+        log.debug(queryStr);
+        Query q = QueryFactory.create(queryStr);
+        QueryExecution qe = QueryExecutionFactory.create(q, union);
+        WebappDaoFactory wadf = new WebappDaoFactoryJena(
+                ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, union));
+        ObjectPropertyDao opDao = wadf.getObjectPropertyDao();
+        try {
+            ResultSet rs = qe.execSelect();
+            while (rs.hasNext()) {
+                QuerySolution qsoln = rs.nextSolution();
+                log.debug(qsoln);
+                String opURI = (prop != null) ? prop.getURI() : qsoln.getResource(
+                        "property").getURI();
+                Resource domainRes = qsoln.getResource("domain");
+                String domainURI = (domainRes != null) ? domainRes.getURI() : null;
+                String rangeURI = qsoln.getResource("range").getURI();
+                if (appropriateDomain(domainRes, subject, tboxModel)) {
+                    additionalProps.add(opDao.getObjectPropertyByURIs(
+                        opURI, domainURI, rangeURI));              
+                }
+            }  
+        } finally {
+            qe.close();
+        }
+        return additionalProps;
+    }   
+    
     
     
     public static List<ObjectProperty> getAdditionalFauxSubpropertiesForList(List<ObjectProperty> propList, 
+                                                                         Individual subject, 
                                                                          Model displayModel, 
                                                                          Model tboxModel) {
+        
         List<ObjectProperty> additionalProps = new ArrayList<ObjectProperty>();
         Model union = ModelFactory.createUnion(displayModel, tboxModel);
-        String propQuery = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
-                "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
-                "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
-                "SELECT ?range ?label ?group ?customForm WHERE { \n" +
-        		"    ?p rdfs:subPropertyOf ?property . \n" +
-                "    ?context config:configContextFor ?p . \n" +
-        		"    ?context config:qualifiedBy ?range . \n" +
-                "    ?context config:hasConfiguration ?configuration . \n" +
-        		"    OPTIONAL { ?configuration config:propertyGroup ?group } \n" +
-                "    OPTIONAL { ?configuration config:displayName ?label } \n" +
-                "    OPTIONAL { ?configuration vitro:customEntryFormAnnot ?customForm } \n" +
-        		"}"; 
-      
-        for (ObjectProperty op : propList) {
-            log.debug("Checking " + op.getURI() + " for additional properties");
-            String queryStr = propQuery.replaceAll("\\?property", "<" + op.getURI() + ">");
-            log.debug(queryStr);
-            Query q = QueryFactory.create(queryStr);
-            QueryExecution qe = QueryExecutionFactory.create(q, union);
-            try {
-                ResultSet rs = qe.execSelect();
-                while (rs.hasNext()) {
-                    ObjectProperty newProp = new ObjectProperty();
-                    newProp.setURI(op.getURI());
-                    QuerySolution qsoln = rs.nextSolution();
-                    log.debug(qsoln);
-                    Resource rangeRes = qsoln.getResource("range");
-                    if (rangeRes != null) {
-                        newProp.setRangeVClassURI(rangeRes.getURI());
-                    } else {
-                        newProp.setRangeVClassURI(op.getRangeVClassURI());
-                    }
-                    Resource groupRes = qsoln.getResource("group");
-                    if (groupRes != null) {
-                        newProp.setGroupURI(groupRes.getURI());
-                    } else {
-                        newProp.setGroupURI(op.getURI());
-                    }
-                    Literal labelLit = qsoln.getLiteral("label");
-                    if (labelLit != null) {
-                        newProp.setDomainPublic(labelLit.getLexicalForm());
-                    } else {
-                        newProp.setDomainPublic(op.getDomainPublic());
-                    }
-                    Literal customFormLit = qsoln.getLiteral("customForm");
-                    if (customFormLit != null) {
-                        newProp.setCustomEntryForm(customFormLit.getLexicalForm());
-                    } else {
-                        newProp.setCustomEntryForm(op.getCustomEntryForm());
-                    }
-                    additionalProps.add(newProp);
-                }  
-            } finally {
-                qe.close();
-            }
-        }
         
+        for (ObjectProperty op : propList) {
+            additionalProps.addAll(getAdditionalFauxSubproperties(op, subject, tboxModel, union));
+        }    
+
         return additionalProps;
     }
     
-    
+    private static boolean appropriateDomain(Resource domainRes, Individual subject, Model tboxModel) {
+        if (subject == null || domainRes == null) {
+            return true;
+        }
+        for (VClass vclass : subject.getVClasses()) {
+            if ((vclass.getURI() != null) &&
+                    ((vclass.getURI().equals(domainRes.getURI()) ||
+                    (tboxModel.contains(
+                            ResourceFactory.createResource(
+                                    vclass.getURI()), RDFS.subClassOf, domainRes))))) {
+                return true;
+            }
+        }
+        return false;
+    }
     
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/edit/EditConfigurationTemplateModel.java

@@ -453,10 +453,13 @@ public class EditConfigurationTemplateModel extends BaseTemplateModel {
 		String objectKey = vreq.getParameter("objectKey");
 		statementDisplay.put(objectKey, objectUri);
 		
+		ObjectProperty predicate = new ObjectProperty();
+		predicate.setURI(predicateUri);
+		
 		//Using object property statement template model here
 		ObjectPropertyStatementTemplateModel osm = new ObjectPropertyStatementTemplateModel(
 				subjectUri, 
-				predicateUri, 
+				predicate, 
 				objectKey, 
 		        statementDisplay, 
 		        null, vreq);
@@ -524,15 +527,23 @@ public class EditConfigurationTemplateModel extends BaseTemplateModel {
     	if( subjectVClasses == null ) {
     		vclasses = wdf.getVClassDao().getAllVclasses();
     	} else if (rangeClass != null) {
+    	    List<VClass> rangeVClasses = new ArrayList<VClass>();
     	    vclasses = new ArrayList<VClass>();
-    	    vclasses.add(rangeClass);
+    	    if (!rangeClass.isUnion()) {    	        
-    	    List<String> subURIs = wdf.getVClassDao().getSubClassURIs(rangeClass.getURI());
+    	        rangeVClasses.add(rangeClass);
-    	    for (String subClassURI : subURIs) {
+    	    } else {
-    	        VClass subClass = wdf.getVClassDao().getVClassByURI(subClassURI);
+    	        rangeVClasses.addAll(rangeClass.getUnionComponents());
-    	        if (subClass != null) {
+    	    }
-    	            vclasses.add(subClass);
+            for(VClass rangeVClass : rangeVClasses) {	
-    	        }
+                vclasses.add(rangeVClass);
-    	   }
+        	    List<String> subURIs = wdf.getVClassDao().getSubClassURIs(rangeVClass.getURI());
+        	    for (String subClassURI : subURIs) {
+        	        VClass subClass = wdf.getVClassDao().getVClassByURI(subClassURI);
+        	        if (subClass != null) {
+        	            vclasses.add(subClass);
+        	        }
+        	    }
+            }
     	} else {
     		//this hash is used to make sure there are no duplicates in the vclasses
     		//a more elegant method may look at overriding equals/hashcode to enable a single hashset of VClass objects

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

@@ -117,7 +117,7 @@ public abstract class BaseIndividualTemplateModel extends BaseTemplateModel {
 				RequestActionConstants.SOME_URI);
 		AddObjectPropertyStatement aops = new AddObjectPropertyStatement(
 				vreq.getJenaOntModel(), individual.getURI(),
-				RequestActionConstants.SOME_URI,
+				RequestActionConstants.SOME_PREDICATE,
 				RequestActionConstants.SOME_URI);
     	return PolicyHelper.isAuthorizedForActions(vreq, new Actions(adps).or(aops));
     }

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

@@ -18,6 +18,7 @@ import org.apache.commons.logging.LogFactory;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
@@ -58,7 +59,7 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
             postprocess(statementData);
             
             /* Collate the data */
-           subclasses = collate(subjectUri, propertyUri, statementData, editing);
+           subclasses = collate(subjectUri, op, statementData, editing);
             
            for (SubclassTemplateModel subclass : subclasses) {
                List<ObjectPropertyStatementTemplateModel> list = subclass.getStatements();
@@ -188,7 +189,7 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
     }
     
     // Collate the statements by subclass. 
-    private List<SubclassTemplateModel> collate(String subjectUri, String propertyUri,
+    private List<SubclassTemplateModel> collate(String subjectUri, ObjectProperty property,
             List<Map<String, String>> statementData, boolean editing) {
   
         String objectKey = getObjectKey();
@@ -218,7 +219,7 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
             }
 
             listForThisSubclass.add(new ObjectPropertyStatementTemplateModel(subjectUri, 
-                    propertyUri, objectKey, map, getTemplateName(), vreq));
+                    property, objectKey, map, getTemplateName(), vreq));
 
         } 
         

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

@@ -13,12 +13,14 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.DropDataPr
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.RdfLiteralHash;
 
+
 public class DataPropertyStatementTemplateModel extends PropertyStatementTemplateModel {
     private static final Log log = LogFactory.getLog(DataPropertyStatementTemplateModel.class); 
     
@@ -28,9 +30,10 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
     private final String templateName;
 
     //Extended to include vitro request to check for special parameters
-    public DataPropertyStatementTemplateModel(String subjectUri, String propertyUri, Literal literal,
+    public DataPropertyStatementTemplateModel(String subjectUri, Property property, Literal literal,
             String templateName, VitroRequest vreq) {
-        super(subjectUri, propertyUri, vreq);
+        
+        super(subjectUri, property, vreq);
         
         this.literalValue = literal;
         this.templateName = templateName;
@@ -50,7 +53,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
         
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "datapropKey", makeHash(dps),
                 "cmd", "delete");
         
@@ -63,7 +66,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
 	private String makeEditUrl() {
         // vitro:moniker is deprecated. We display existing data values so editors can 
         // move them to other properties and delete, but don't allow editing.
-        if ( propertyUri.equals(VitroVocabulary.MONIKER) ) {
+        if ( VitroVocabulary.MONIKER.equals(property.getURI()) ) {
             return "";           
         }
         
@@ -76,7 +79,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
         
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "datapropKey", makeHash(dps));
         
         if ( deleteUrl.isEmpty() ) {
@@ -89,7 +92,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
 	}
         
 	private DataPropertyStatement makeStatement() {
-		DataPropertyStatement dps = new DataPropertyStatementImpl(subjectUri, propertyUri, literalValue.getLexicalForm());
+		DataPropertyStatement dps = new DataPropertyStatementImpl(subjectUri, property.getURI(), literalValue.getLexicalForm());
 		// Language and datatype are needed to get the correct hash value
 		dps.setLanguage(literalValue.getLanguage());
 		dps.setDatatypeURI(literalValue.getDatatypeURI());

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

@@ -88,7 +88,7 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
             DataPropertyStatementDao dpDao = vreq.getWebappDaoFactory().getDataPropertyStatementDao();
             List<Literal> values = dpDao.getDataPropertyValuesForIndividualByProperty(subject, dp, queryString, constructQueries);            
             for (Literal value : values) {
-                statements.add(new DataPropertyStatementTemplateModel(subjectUri, propertyUri, value, getTemplateName(), vreq));
+                statements.add(new DataPropertyStatementTemplateModel(subjectUri, dp, value, getTemplateName(), vreq));
             }
         } else {
             log.debug("Data property " + getUri() + " is unpopulated.");

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

@@ -1,94 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
-
-import java.util.Arrays;
-import java.util.List;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-
-/**
- * Sometimes we don't want to show an Add, Edit, or Delete link for a particular
- * property, no matter who the user is.
- * 
- * TODO These are hard-coded while we wait for the Application Ontology to be
- * implemented.
- */
-public class EditLinkSuppressor {
-	private static final Log log = LogFactory.getLog(EditLinkSuppressor.class);
-
-	private static final String CORE = "http://vivoweb.org/ontology/core#";
-	private static final String PUB_TO_AUTHORSHIP = core("informationResourceInAuthorship");
-	private static final String PERSON_TO_AUTHORSHIP = core("authorInAuthorship");
-	private static final String AUTHORSHIP_TO_PERSON = core("linkedAuthor");
-	private static final String AUTHORSHIP_TO_PUB = core("linkedInformationResource");
-	private static final String INDIVIDUAL_TO_WEBPAGE = core("webpage");
-	private static final String WEBPAGE_TO_INDIVIDUAL = core("webpageOf");
-	private static final String HAS_RESEARCH_AREA = core("hasResearchArea");
-	private static final String HAS_SUBJECT_AREA = core("hasSubjectArea");
-	private static final String RESEARCH_AREA_OF = core("researchAreaOf");
-	private static final String SUBJECT_AREA_FOR = core("subjectAreaFor");
-
-	private static String core(String localName) {
-		return CORE + localName;
-	}
-
-	private static final List<String> suppressAddLinksForThese = Arrays
-			.asList(new String[] { AUTHORSHIP_TO_PERSON, AUTHORSHIP_TO_PUB,
-					WEBPAGE_TO_INDIVIDUAL });
-
-	private static final List<String> suppressEditLinksForThese = Arrays
-			.asList(new String[] { WEBPAGE_TO_INDIVIDUAL });
-
-	private static final List<String> suppressDeleteLinksForThese = Arrays
-			.asList(new String[] { PUB_TO_AUTHORSHIP, PERSON_TO_AUTHORSHIP,
-					AUTHORSHIP_TO_PERSON, AUTHORSHIP_TO_PUB,
-					INDIVIDUAL_TO_WEBPAGE, WEBPAGE_TO_INDIVIDUAL,
-					HAS_RESEARCH_AREA, RESEARCH_AREA_OF, HAS_SUBJECT_AREA,
-					SUBJECT_AREA_FOR });
-
-	// TODO When we remove the hard-coding, vreq will allow us to find the
-	// application ontology model.
-	@SuppressWarnings("unused")
-	private final VitroRequest vreq;
-
-	public EditLinkSuppressor(VitroRequest vreq) {
-		this.vreq = vreq;
-	}
-
-	/**
-	 * Should we suppress the Add link on this property?
-	 */
-	public boolean isAddLinkSuppressed(String propertyUri) {
-		if (propertyUri == null) {
-			log.error("Suppressing the add link on a null property.");
-			return true;
-		}
-		return suppressAddLinksForThese.contains(propertyUri);
-	}
-
-	/**
-	 * Should we suppress the Edit link on this property?
-	 */
-	public boolean isEditLinkSuppressed(String propertyUri) {
-		if (propertyUri == null) {
-			log.error("Suppressing the edit link on a null property.");
-			return true;
-		}
-		return suppressEditLinksForThese.contains(propertyUri);
-	}
-
-	/**
-	 * Should we suppress the Delete link on this property?
-	 */
-	public boolean isDeleteLinkSuppressed(String propertyUri) {
-		if (propertyUri == null) {
-			log.error("Suppressing the delete link on a null property.");
-			return true;
-		}
-		return suppressDeleteLinksForThese.contains(propertyUri);
-	}
-}

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

@@ -20,6 +20,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
@@ -74,12 +75,12 @@ public class GroupedPropertyList extends BaseTemplateModel {
         List<ObjectProperty> populatedObjectPropertyList = subject
                 .getPopulatedObjectPropertyList();
         
-        List<ObjectProperty> additions = ApplicationConfigurationOntologyUtils
+        Collection<ObjectProperty> additions = ApplicationConfigurationOntologyUtils
                 .getAdditionalFauxSubpropertiesForList(
-                        populatedObjectPropertyList, vreq);
+                        populatedObjectPropertyList, subject, vreq);
         if (log.isDebugEnabled()) {
             for (ObjectProperty t : additions) {
-                log.debug(t.getDomainPublic() + " " + t.getGroupURI());
+                log.debug(t.getDomainPublic() + " " + t.getGroupURI() + " domain " + t.getDomainVClassURI());
             }
             log.debug("Added " + additions.size() + 
                     " properties due to application configuration ontology");
@@ -88,7 +89,7 @@ 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
         // unpopulated, so the properties are displayed to allow statements to be added to these properties.
         // RY In future, we should limit this to properties that the user has permission to add properties to.
@@ -175,7 +176,13 @@ public class GroupedPropertyList extends BaseTemplateModel {
         // There is no ObjectPropertyDao.getAllPossibleObjectPropertiesForIndividual() parallel to 
         // DataPropertyDao.getAllPossibleDatapropsForIndividual(). The comparable method for object properties
         // is defined using PropertyInstance rather than ObjectProperty.
-        PropertyInstanceDao piDao = wdf.getPropertyInstanceDao();
+        
+        // Getting WebappDaoFactory from the session because we can't have the filtering
+        // that gets applied to the request.  This breaks blank node structures in the
+        // restrictions that determine applicable properties.
+        WebappDaoFactory wadf = ModelAccess.on(vreq.getSession().getServletContext()).getWebappDaoFactory();
+        PropertyInstanceDao piDao = wadf.getPropertyInstanceDao();
+        
         Collection<PropertyInstance> allPropInstColl = piDao
                 .getAllPossiblePropInstForIndividual(subject.getURI());
         if (allPropInstColl != null) {
@@ -183,7 +190,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
                 if (pi != null) {
                     if (!alreadyOnObjectPropertyList(
                             populatedObjectPropertyList, pi)) {
-                        addObjectPropertyToPropertyList(pi.getPropertyURI(), pi.getRangeClassURI(),
+                        addObjectPropertyToPropertyList(pi.getPropertyURI(), pi.getDomainClassURI(), pi.getRangeClassURI(),
                                 propertyList);
                     }
                 } else {
@@ -199,7 +206,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
         // constitute a special case (i.e., included in piDao.getAllPossiblePropInstForIndividual()).
         for (String propertyUri : VITRO_PROPS_TO_ADD_TO_LIST) {
             if (!alreadyOnPropertyList(propertyList, propertyUri)) {
-                addObjectPropertyToPropertyList(propertyUri, null, propertyList);
+                addObjectPropertyToPropertyList(propertyUri, null, null, propertyList);
             }
         }
     }
@@ -211,16 +218,29 @@ public class GroupedPropertyList extends BaseTemplateModel {
         }
         for (ObjectProperty op : opList) {
             if (op.getURI() != null && op.getURI().equals(pi.getPropertyURI())) {
-                return true;
+                if(op.getDomainVClassURI() == null) {
+                    if(pi.getDomainClassURI() == null) {
+                        return true;   
+                    }
+                } else if (op.getDomainVClassURI().equals(pi.getDomainClassURI())) {
+                    return true;
+                }
+                if(op.getRangeVClassURI() == null) {
+                    if (pi.getDomainClassURI() == null) {
+                        return true;
+                    }
+                } else if (op.getRangeVClassURI().equals(pi.getRangeClassURI())) {
+                    return true;
+                }
             }
         }
         return false;
     }
 
-    private void addObjectPropertyToPropertyList(String propertyUri, String rangeUri,
+    private void addObjectPropertyToPropertyList(String propertyUri, String domainUri, String rangeUri,
             List<Property> propertyList) {
         ObjectPropertyDao opDao = wdf.getObjectPropertyDao();
-        ObjectProperty op = opDao.getObjectPropertyByURIAndRangeURI(propertyUri, rangeUri);
+        ObjectProperty op = opDao.getObjectPropertyByURIs(propertyUri, domainUri, rangeUri);
         if (op == null) {
             log.error("ObjectProperty op returned null from opDao.getObjectPropertyByURI(" + propertyUri + ")");
         } else if (op.getURI() == null) {
@@ -457,11 +477,16 @@ public class GroupedPropertyList extends BaseTemplateModel {
     }
 
     public PropertyTemplateModel pullProperty(String propertyUri) {
+        return pullProperty(propertyUri, null);
+    }
+    
+    public PropertyTemplateModel pullProperty(String propertyUri, String rangeUri) {
 
         for (PropertyGroupTemplateModel pgtm : groups) {
             List<PropertyTemplateModel> properties = pgtm.getProperties();
             for (PropertyTemplateModel ptm : properties) {
-                if (propertyUri.equals(ptm.getUri())) {
+                if (propertyUri.equals(ptm.getUri()) && 
+                        (rangeUri == null || rangeUri.equals(ptm.getRangeUri()))) {
                     // Remove the property from the group.
                     // NB Works with a for-each loop instead of an iterator,
                     // since iteration doesn't continue after the remove.

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

@@ -14,6 +14,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAct
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
@@ -37,7 +38,7 @@ public class NameStatementTemplateModel extends PropertyStatementTemplateModel {
     private final String editUrl;
 
     NameStatementTemplateModel(String subjectUri, VitroRequest vreq) {
-        super(subjectUri, VitroVocabulary.LABEL, vreq);
+        super(subjectUri, new Property(VitroVocabulary.LABEL), vreq);
 
         // NIHVIVO-2466 Use the same methods to get the label that are used elsewhere in the 
         // application, to guarantee consistent results for individuals with multiple labels
@@ -69,7 +70,7 @@ public class NameStatementTemplateModel extends PropertyStatementTemplateModel {
         
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "datapropKey", makeHash(dps),
                 "deleteProhibited", "prohibited");
         
@@ -80,7 +81,7 @@ public class NameStatementTemplateModel extends PropertyStatementTemplateModel {
         
 	private DataPropertyStatement makeStatement(Literal literalValue) {
 		DataPropertyStatement dps = new DataPropertyStatementImpl(subjectUri,
-				propertyUri, literalValue.getLexicalForm());
+				property.getURI(), literalValue.getLexicalForm());
 		// Language and datatype are needed to get the correct hash value
 		dps.setLanguage(literalValue.getLanguage());
 		dps.setDatatypeURI(literalValue.getDatatypeURI());

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

@@ -13,8 +13,10 @@ import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAction;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.DropObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatementImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
@@ -31,9 +33,9 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
     private final String editUrl;
     private final String deleteUrl;
     
-    public ObjectPropertyStatementTemplateModel(String subjectUri, String propertyUri, String objectKey, 
+    public ObjectPropertyStatementTemplateModel(String subjectUri, ObjectProperty predicate, String objectKey, 
             Map<String, String> data, String templateName, VitroRequest vreq) {
-        super(subjectUri, propertyUri, vreq);
+        super(subjectUri, predicate, vreq);
 
         this.data = Collections.unmodifiableMap(new HashMap<String, String>(data));
         this.objectUri = data.get(objectKey);        
@@ -41,7 +43,8 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
         //to keep track of later
         this.objectKey = objectKey;
         
-        ObjectPropertyStatement ops = new ObjectPropertyStatementImpl(subjectUri, propertyUri, objectUri);
+        ObjectPropertyStatement ops = new ObjectPropertyStatementImpl(subjectUri, property.getURI(), objectUri);
+        ops.setProperty(predicate);
         
         // Do delete url first, since it is used in building edit url
         this.deleteUrl = makeDeleteUrl();
@@ -50,24 +53,24 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
 
 	private String makeDeleteUrl() {
     	// Is the delete link suppressed for this property?
-    	if (new EditLinkSuppressor(vreq).isDeleteLinkSuppressed(propertyUri)) {
+    	if (property.isDeleteLinkSuppressed()) {
     		return "";
     	}
         
         // Determine whether the statement can be deleted
 		RequestedAction action = new DropObjectPropertyStatement(
-				vreq.getJenaOntModel(), subjectUri, propertyUri, objectUri);
+				vreq.getJenaOntModel(), subjectUri, property, objectUri);
         if ( ! PolicyHelper.isAuthorizedForActions(vreq, action) ) {
             return "";
         }
         
-        if (propertyUri.equals(VitroVocabulary.IND_MAIN_IMAGE)) {
+        if (VitroVocabulary.IND_MAIN_IMAGE.equals(property.getURI())) {
             return ObjectPropertyTemplateModel.getImageUploadUrl(subjectUri, "delete");
         } 
         
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "objectUri", objectUri,
                 "cmd", "delete",
                 "objectKey", objectKey);
@@ -92,7 +95,7 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
 
 	private String makeEditUrl(ObjectPropertyStatement ops) {
     	// Is the edit link suppressed for this property?
-    	if (new EditLinkSuppressor(vreq).isEditLinkSuppressed(propertyUri)) {
+    	if (property.isEditLinkSuppressed()) {
     		return "";
     	}
         
@@ -102,19 +105,26 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
             return "";
         }
         
-        if (propertyUri.equals(VitroVocabulary.IND_MAIN_IMAGE)) {
+        if (VitroVocabulary.IND_MAIN_IMAGE.equals(property.getURI())) {
             return ObjectPropertyTemplateModel.getImageUploadUrl(subjectUri, "edit");
         } 
 
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "objectUri", objectUri);
         
         if ( deleteUrl.isEmpty() ) {
             params.put("deleteProhibited", "prohibited");
         }
         
+        if (ops.getProperty()!= null && ops.getProperty().getDomainVClassURI() != null) {
+            params.put("domainUri", ops.getProperty().getDomainVClassURI());
+        }
+        if (ops.getProperty()!= null && ops.getProperty().getRangeVClassURI() != null) {
+            params.put("rangeUri", ops.getProperty().getRangeVClassURI());
+        }
+        
         params.putAll(UrlBuilder.getModelParams(vreq));
         
         return UrlBuilder.getUrl(EDIT_PATH, params);

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

@@ -80,7 +80,6 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
     private PropertyListConfig config;
     private String objectKey;    
     private String sortDirection;
-    private String rangeURI;
     
     ObjectPropertyTemplateModel(ObjectProperty op, Individual subject, VitroRequest vreq, 
             boolean editing)
@@ -90,7 +89,8 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
         setName(op.getDomainPublic());
         
         sortDirection = op.getDomainEntitySortDirection();
-        rangeURI = op.getRangeVClassURI();
+        domainUri = op.getDomainVClassURI();
+        rangeUri = op.getRangeVClassURI();
         
         // Get the config for this object property
         try {
@@ -110,13 +110,13 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
 
     protected void setAddUrl(Property property) {
     	// Is the add link suppressed for this property?
-    	if (new EditLinkSuppressor(vreq).isAddLinkSuppressed(propertyUri)) {
+    	if (property.isAddLinkSuppressed()) {
     		return;
     	}
         
         // Determine whether a new statement can be added
 		RequestedAction action = new AddObjectPropertyStatement(
-				vreq.getJenaOntModel(), subjectUri, propertyUri,
+				vreq.getJenaOntModel(), subjectUri, property,
 				RequestActionConstants.SOME_URI);
         if ( ! PolicyHelper.isAuthorizedForActions(vreq, action) ) {
             return;
@@ -133,6 +133,9 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
                     "subjectUri", subjectUri,
                     "predicateUri", propertyUri);
             
+            if (domainUri != null) {
+                params.put("domainUri", domainUri);
+            }
             if (rangeUri != null) {
                 params.put("rangeUri", rangeUri);
             }
@@ -157,7 +160,7 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
     
     protected List<Map<String, String>> getStatementData() {
         ObjectPropertyStatementDao opDao = vreq.getWebappDaoFactory().getObjectPropertyStatementDao();
-        return opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, objectKey, rangeURI, getSelectQuery(), getConstructQueries(), sortDirection);
+        return opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, objectKey, domainUri, rangeUri, getSelectQuery(), getConstructQueries(), sortDirection);
     }
     
     protected abstract boolean isEmpty();

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

@@ -36,8 +36,13 @@ public class PropertyGroupTemplateModel extends BaseTemplateModel {
         properties = new ArrayList<PropertyTemplateModel>(propertyList.size());
         for (Property p : propertyList)  {
             if (p instanceof ObjectProperty) {
-                ObjectProperty op = (ObjectProperty)p;
+                ObjectProperty op = (ObjectProperty) p;
-                properties.add(ObjectPropertyTemplateModel.getObjectPropertyTemplateModel(op, subject, vreq, editing, populatedObjectPropertyList));
+                ObjectPropertyTemplateModel tm = ObjectPropertyTemplateModel.getObjectPropertyTemplateModel(
+                        op, subject, vreq, editing, populatedObjectPropertyList);
+                if (!tm.isEmpty() || (editing && !tm.getAddUrl().isEmpty())) {
+                    properties.add(tm);                    
+                }
+
             } else {
                 properties.add(new DataPropertyTemplateModel((DataProperty)p, subject, vreq, editing, populatedDataPropertyList));
             }

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

@@ -2,6 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.BaseTemplateModel;
 
@@ -10,12 +11,12 @@ public abstract class PropertyStatementTemplateModel extends BaseTemplateModel {
 
     protected final VitroRequest vreq;
     protected final String subjectUri;
-    protected final String propertyUri;
+    protected final Property property;
     
-    PropertyStatementTemplateModel(String subjectUri, String propertyUri, VitroRequest vreq) {
+    PropertyStatementTemplateModel(String subjectUri, Property property, VitroRequest vreq) {
         this.vreq = vreq;        
         this.subjectUri = subjectUri;
-        this.propertyUri = propertyUri;              
+        this.property = property;              
     }
     
     /* Template properties */

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

@@ -28,7 +28,10 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
     
     protected final VitroRequest vreq;
     protected final String subjectUri;
+    protected final Property property;
     protected final String propertyUri;
+    protected String domainUri;
+    protected String rangeUri;
     private final String localName;
 
     protected Map<String, Object> verboseDisplay;
@@ -41,6 +44,7 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
     PropertyTemplateModel(Property property, Individual subject, VitroRequest vreq) {
         this.vreq = vreq;
         subjectUri = subject.getURI(); 
+        this.property = property;
         propertyUri = property.getURI();
         localName = property.getLocalName();
         setVerboseDisplayValues(property);
@@ -121,6 +125,10 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
         return propertyUri;
     }
     
+    public String getRangeUri() {
+        return rangeUri;
+    }
+    
     public String getAddUrl() {
         //log.info("addUrl=" + addUrl);
         return (addUrl != null) ? addUrl : "";

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

@@ -41,7 +41,7 @@ public class UncollatedObjectPropertyTemplateModel extends ObjectPropertyTemplat
             String objectKey = getObjectKey();
             for (Map<String, String> map : statementData) {
                 statements.add(new ObjectPropertyStatementTemplateModel(subjectUri, 
-                        propertyUri, objectKey, map, getTemplateName(), vreq));
+                        op, objectKey, map, getTemplateName(), vreq));
             }
             
             postprocessStatementList(statements);

webapp/test/edu/cornell/mannlib/vitro/webapp/auth/policy/SelfEditingPolicyTest.java

@@ -42,6 +42,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.DropObject
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 
 public class SelfEditingPolicyTest extends AbstractTestClass {
@@ -55,8 +56,8 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 	private static final String UNSAFE_RESOURCE = UNSAFE_NS
 			+ "otherIndividual99999";
 
-	private static final String SAFE_PREDICATE = SAFE_NS + "hasHairStyle";
+	private static final Property SAFE_PREDICATE = new Property(SAFE_NS + "hasHairStyle");
-	private static final String UNSAFE_PREDICATE = UNSAFE_NS + "hasSuperPowers";
+	private static final Property UNSAFE_PREDICATE = new Property(UNSAFE_NS + "hasSuperPowers");
 
 	private ServletContextStub ctx;
 
@@ -95,19 +96,19 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 		PropertyRestrictionPolicyHelper.setBean(ctx, prph);
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SELFEDITOR_URI,
-				"http://mannlib.cornell.edu/bad#prp234", SAFE_RESOURCE);
+				new Property("http://mannlib.cornell.edu/bad#prp234"), SAFE_RESOURCE);
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SAFE_RESOURCE,
-				"http://mannlib.cornell.edu/bad#prp234", SELFEDITOR_URI);
+				new Property("http://mannlib.cornell.edu/bad#prp234"), SELFEDITOR_URI);
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SELFEDITOR_URI,
-				"http://mannlib.cornell.edu/bad#prp999", SAFE_RESOURCE);
+				new Property("http://mannlib.cornell.edu/bad#prp999"), SAFE_RESOURCE);
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SAFE_RESOURCE,
-				"http://mannlib.cornell.edu/bad#prp999", SELFEDITOR_URI);
+				new Property("http://mannlib.cornell.edu/bad#prp999"), SELFEDITOR_URI);
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SAFE_RESOURCE,
@@ -132,11 +133,11 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddDataPropertyStatement(ontModel, SELFEDITOR_URI,
-				SAFE_PREDICATE);
+				SAFE_PREDICATE.getURI());
 		assertDecision(AUTHORIZED, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddDataPropertyStatement(ontModel, SELFEDITOR_URI,
-				UNSAFE_PREDICATE);
+				UNSAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 	}
 
@@ -218,16 +219,16 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 	//
 	@Test
 	public void testVisitIdentifierBundleEditDataPropStmt() {
-		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI,SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI,SAFE_PREDICATE.getURI());
 		assertDecision(AUTHORIZED, policy.isAuthorized(ids, whatToAuth));
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI, UNSAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI, UNSAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, UNSAFE_RESOURCE, SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, UNSAFE_RESOURCE, SAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, SAFE_RESOURCE, SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SAFE_RESOURCE, SAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 	}
 
@@ -287,7 +288,7 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 	public void twoSEIsFindDataPropertySubject() {
 		setUpTwoSEIs();
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI, SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI, SAFE_PREDICATE.getURI());
 		assertDecision(AUTHORIZED, policy.isAuthorized(ids, whatToAuth));
 	}
 
@@ -295,7 +296,7 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 	public void twoSEIsDontFindInDataProperty() {
 		setUpTwoSEIs();
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, SAFE_RESOURCE, SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SAFE_RESOURCE, SAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 	}
 

webapp/test/edu/cornell/mannlib/vitro/webapp/auth/policy/SelfEditingPolicy_2_Test.java

@@ -32,6 +32,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPr
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 
 public class SelfEditingPolicy_2_Test extends AbstractTestClass {
@@ -123,7 +124,7 @@ public class SelfEditingPolicy_2_Test extends AbstractTestClass {
 	@Test
 	public void nullIdentifierBundle() {
 		AddObjectPropertyStatement whatToAuth = new AddObjectPropertyStatement(
-				ontModel, SELFEDITOR_URI, SAFE_PREDICATE, SAFE_RESOURCE);
+				ontModel, SELFEDITOR_URI, new Property(SAFE_PREDICATE), SAFE_RESOURCE);
 		PolicyDecision dec = policy.isAuthorized(null, whatToAuth);
 		Assert.assertNotNull(dec);
 		Assert.assertEquals(Authorization.INCONCLUSIVE, dec.getAuthorized());
@@ -277,7 +278,7 @@ public class SelfEditingPolicy_2_Test extends AbstractTestClass {
 	private void assertAddObjectPropStmt(String uriOfSub, String uriOfPred,
 			String uriOfObj, Authorization expectedAuthorization) {
 		AddObjectPropertyStatement whatToAuth = new AddObjectPropertyStatement(
-				ontModel, uriOfSub, uriOfPred, uriOfObj);
+				ontModel, uriOfSub, new Property(uriOfPred), uriOfObj);
 		PolicyDecision dec = policy.isAuthorized(ids, whatToAuth);
 		log.debug(dec);
 		Assert.assertNotNull(dec);
@@ -291,7 +292,7 @@ public class SelfEditingPolicy_2_Test extends AbstractTestClass {
 	private void assertEditObjPropStmt(String uriOfSub, String uriOfPred,
 			String uriOfObj, Authorization expectedAuthorization) {
 		EditObjectPropertyStatement whatToAuth = new EditObjectPropertyStatement(
-				ontModel, uriOfSub, uriOfPred, uriOfObj);
+				ontModel, uriOfSub, new Property(uriOfPred), uriOfObj);
 		PolicyDecision dec = policy.isAuthorized(ids, whatToAuth);
 		log.debug(dec);
 		Assert.assertNotNull(dec);

webapp/test/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelperTest.java

@@ -18,7 +18,6 @@ import java.util.Map;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.apache.log4j.Level;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -27,6 +26,8 @@ import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.sdb.util.Pair;
+import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean;
@@ -58,17 +59,25 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 //		setLoggerLevel(PropertyRestrictionPolicyHelper.class, Level.DEBUG);
 	}
 
+	private void mapPut(String predicateURI, RoleLevel roleLevel, 
+	                    Map<Pair<String, Pair<String,String>>, RoleLevel> map) { 
+	    map.put(new Pair<String, Pair<String,String>>(
+	            OWL.Thing.getURI(), new Pair<String, String>(
+	                    predicateURI, OWL.Thing.getURI())), roleLevel);
+	}
+	
 	@Before
 	public void createTheBean() {
-		Map<String, RoleLevel> displayLevels = new HashMap<String, BaseResourceBean.RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> displayLevels = 
-		displayLevels.put("http://predicates#display_self", SELF);
+		        new HashMap<Pair<String, Pair<String,String>>, RoleLevel>();
-		displayLevels.put("http://predicates#display_curator", CURATOR);
+		mapPut("http://predicates#display_curator", CURATOR, displayLevels);
-		displayLevels.put("http://predicates#display_hidden", NOBODY);
+		mapPut("http://predicates#display_hidden", NOBODY, displayLevels);
 
-		Map<String, RoleLevel> modifyLevels = new HashMap<String, BaseResourceBean.RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> modifyLevels = 
-		modifyLevels.put("http://predicates#modify_self", SELF);
+		        new HashMap<Pair<String, Pair<String,String>>, RoleLevel>();
-		modifyLevels.put("http://predicates#modify_curator", CURATOR);
+		mapPut("http://predicates#modify_self", SELF, modifyLevels);
-		modifyLevels.put("http://predicates#modify_hidden", NOBODY);
+		mapPut("http://predicates#modify_curator", CURATOR, modifyLevels);
+		mapPut("http://predicates#modify_hidden", NOBODY, modifyLevels);
 
 		bean = new PropertyRestrictionPolicyHelper(
 				Arrays.asList(PROHIBITED_NAMESPACES),
@@ -125,68 +134,75 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 	@Test
 	public void displayPredicateNoRestriction() {
 		assertEquals("displayPredicate: open", true,
-				bean.canDisplayPredicate("http://predicates#open", PUBLIC));
+				bean.canDisplayPredicate(createVitroProperty(
+				        "http://predicates#open"), PUBLIC));
 	}
 
 	@Test
 	public void displayPredicateRestrictionLower() {
 		assertEquals("displayPredicate: lower restriction", true,
-				bean.canDisplayPredicate("http://predicates#display_self",
+				bean.canDisplayPredicate(createVitroProperty(
-						CURATOR));
+				        "http://predicates#display_self"), CURATOR));
 	}
 
 	@Test
 	public void displayPredicateRestrictionEqual() {
 		assertEquals("displayPredicate: equal restriction", true,
-				bean.canDisplayPredicate("http://predicates#display_curator",
+				bean.canDisplayPredicate(createVitroProperty(
-						CURATOR));
+				        "http://predicates#display_curator"), CURATOR));
 	}
 
 	@Test
 	public void displayPredicateRestrictionHigher() {
 		assertEquals("displayPredicate: higher restriction", false,
-				bean.canDisplayPredicate("http://predicates#display_hidden",
+				bean.canDisplayPredicate(createVitroProperty(
-						CURATOR));
+				        "http://predicates#display_hidden"), CURATOR));
 	}
 
 	@Test
 	public void modifyPredicateNoRestriction() {
 		assertEquals("modifyPredicate: open", true,
-				bean.canModifyPredicate("http://predicates#open", PUBLIC));
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        "http://predicates#open"), PUBLIC));
 	}
 
 	@Test
 	public void modifyPredicateRestrictionLower() {
 		assertEquals("modifyPredicate: lower restriction", true,
-				bean.canModifyPredicate("http://predicates#modify_self",
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        "http://predicates#modify_self"),
 						CURATOR));
 	}
 
 	@Test
 	public void modifyPredicateRestrictionEqual() {
 		assertEquals("modifyPredicate: equal restriction", true,
-				bean.canModifyPredicate("http://predicates#modify_curator",
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        "http://predicates#modify_curator"),
 						CURATOR));
 	}
 
 	@Test
 	public void modifyPredicateRestrictionHigher() {
 		assertEquals("modifyPredicate: higher restriction", false,
-				bean.canModifyPredicate("http://predicates#modify_hidden",
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        "http://predicates#modify_hidden"),
 						CURATOR));
 	}
 
 	@Test
 	public void modifyPredicateProhibitedNamespace() {
 		assertEquals("modifyPredicate: prohibited namespace", false,
-				bean.canModifyPredicate(PROHIBITED_NAMESPACES[0] + "randoom",
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        PROHIBITED_NAMESPACES[0] + "randoom"),
 						DB_ADMIN));
 	}
 
 	@Test
 	public void modifyPredicatePermittedException() {
 		assertEquals("modifyPredicate: permitted exception", true,
-				bean.canModifyPredicate(PERMITTED_EXCEPTIONS[0], DB_ADMIN));
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        PERMITTED_EXCEPTIONS[0]), DB_ADMIN));
 	}
 
 	// ----------------------------------------------------------------------
@@ -195,9 +211,10 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 
 	@Test
 	public void buildDisplayThresholds() {
-		Map<String, RoleLevel> expectedMap = new HashMap<String, BaseResourceBean.RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, BaseResourceBean.RoleLevel> expectedMap = 
-		expectedMap.put("http://thresholds#display_public", PUBLIC);
+		        new HashMap<Pair<String, Pair<String,String>>, BaseResourceBean.RoleLevel>();
-		expectedMap.put("http://thresholds#display_hidden", NOBODY);
+		mapPut("http://thresholds#display_public", PUBLIC, expectedMap);
+		mapPut("http://thresholds#display_hidden", NOBODY, expectedMap);
 
 		Map<String, RoleLevel> actualMap = populateThresholdMap(PROPERTY_DISPLAY_THRESHOLD);
 		assertEquals("display thresholds", expectedMap, actualMap);
@@ -205,9 +222,10 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 
 	@Test
 	public void buildModifyThresholds() {
-		Map<String, RoleLevel> expectedMap = new HashMap<String, BaseResourceBean.RoleLevel>();
+	    Map<Pair<String, Pair<String,String>>, BaseResourceBean.RoleLevel> expectedMap = 
-		expectedMap.put("http://thresholds#modify_editor", EDITOR);
+                new HashMap<Pair<String, Pair<String,String>>, BaseResourceBean.RoleLevel>();
-		expectedMap.put("http://thresholds#modify_curator", CURATOR);
+		mapPut("http://thresholds#modify_editor", EDITOR, expectedMap);
+		mapPut("http://thresholds#modify_curator", CURATOR, expectedMap);
 
 		Map<String, RoleLevel> actualMap = populateThresholdMap(PROPERTY_MODIFY_THRESHOLD);
 		assertEquals("modify thresholds", expectedMap, actualMap);
@@ -244,4 +262,9 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 			model.add(subject, property, object);
 		}
 	}
+	
+	private edu.cornell.mannlib.vitro.webapp.beans.Property createVitroProperty(
+	        String propertyURI) {
+	    return new edu.cornell.mannlib.vitro.webapp.beans.Property(propertyURI);
+	}
 }

webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerInversePropertyTest.java

@@ -81,7 +81,14 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
 		aBox.add(a,P,b);		
 		Assert.assertTrue(inf.contains(b,Q,a));				
 		aBox.add(c,Q,d);		
-		Assert.assertTrue(inf.contains(d,P,c));	       
+		Assert.assertTrue(inf.contains(d,P,c));	      
+		
+		// delete assertions and verify that inferences go away
+		aBox.remove(c,Q,d);
+		Assert.assertFalse(inf.contains(d,P,c));
+		aBox.remove(a,P,b);
+		Assert.assertFalse(inf.contains(b,Q,a));
+		
 	}
 
     @Test

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelperStub.java

@@ -10,6 +10,8 @@ import java.util.Set;
 
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.sdb.util.Pair;
+import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.webapp.auth.policy.bean.PropertyRestrictionPolicyHelper;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
@@ -43,10 +45,15 @@ public class PropertyRestrictionPolicyHelperStub extends
 			namespaceSet.addAll(Arrays.asList(restrictedNamespaces));
 		}
 		
-		Map<String, RoleLevel> thresholdMap = new HashMap<String, RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> thresholdMap = new HashMap<
+		        Pair<String, Pair<String,String>>, RoleLevel>();
 		if (restrictedProperties != null) {
 			for (String prop : restrictedProperties) {
-				thresholdMap.put(prop, RoleLevel.NOBODY);
+				thresholdMap.put(
+				        new Pair<String, Pair<String, String>>(
+				                OWL.Thing.getURI(), new Pair<String, String>(
+				                        prop, OWL.Thing.getURI())), 
+				                                RoleLevel.NOBODY);
 			}
 		}
 		
@@ -57,8 +64,8 @@ public class PropertyRestrictionPolicyHelperStub extends
 	private PropertyRestrictionPolicyHelperStub(
 			Set<String> modifyRestrictedNamespaces,
 			Set<String> modifyPermittedExceptions,
-			Map<String, RoleLevel> displayThresholds,
+			Map<Pair<String, Pair<String,String>>, RoleLevel> displayThresholds,
-			Map<String, RoleLevel> modifyThresholds) {
+			Map<Pair<String, Pair<String,String>>, RoleLevel> modifyThresholds) {
 		super(modifyRestrictedNamespaces, modifyPermittedExceptions,
 				displayThresholds, modifyThresholds, ModelFactory.createDefaultModel());
 	}

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

@@ -67,7 +67,7 @@ public class ObjectPropertyDaoStub implements ObjectPropertyDao {
 	}
 	
     @Override
-    public ObjectProperty getObjectPropertyByURIAndRangeURI(String objectPropertyURI, String rangeURI) {
+    public ObjectProperty getObjectPropertyByURIs(String objectPropertyURI, String domainURI, String rangeURI) {
         return getObjectPropertyByURI(objectPropertyURI);
     }
 

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

@@ -216,7 +216,7 @@ public class ObjectPropertyStatementDaoStub implements
 
 	@Override
 	public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
-			String subjectUri, String propertyUri, String objectKey, String rangeUri,
+			String subjectUri, String propertyUri, String objectKey, String domainUri, String rangeUri,
 			String query, Set<String> constructQueries, String sortDir) {
 		throw new RuntimeException(
 				"ObjectPropertyStatementDaoStub.getObjectPropertyStatementsForIndividualByProperty() not implemented.");

webapp/web/WEB-INF/resources/startup_listeners.txt

@@ -25,8 +25,6 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.UserModelSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ContentModelSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ModelMakerSetup
 
-edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase
-
 edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorageSetup
 
 edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil$Setup
@@ -38,6 +36,8 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup
 
 edu.cornell.mannlib.vitro.webapp.servlet.setup.SimpleReasonerSetup
 
+edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase
+
 # Must run after JenaDataSourceSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ThemeInfoSetup
 

webapp/web/i18n/all.properties

@@ -42,13 +42,13 @@ crop_page_title_with_name = Crop image for {0}
 current_photo = Current Photo
 upload_photo = Upload a photo
 replace_photo = Replace Photo
-photo_types =  (JPEG, GIF or PNG)
+photo_types = (JPEG, GIF or PNG)
 maximum_file_size = Maximum file size: {0} megabytes
 minimum_image_dimensions = Minimum image dimensions: {0} x {1} pixels
 
 cropping_caption = Your profile photo will look like the image below.
 cropping_note = To make adjustments, you can drag around and resize the photo to the right. \
-                When you are happy with your photo click the "Save Photo" button.
+When you are happy with your photo click the "Save Photo" button.
 
 alt_thumbnail_photo = Individual photo
 alt_image_to_crop = Image to be cropped
@@ -69,7 +69,7 @@ imageUpload.errorFileTooBig = Please upload an image smaller than {0} megabytes.
 imageUpload.errorUnrecognizedFileType = ''{0}'' is not a recognized image file type. Please upload JPEG, GIF, or PNG files only.
 imageUpload.errorNoPhotoSelected = Please browse and select a photo.
 imageUpload.errorBadMultipartRequest = Failed to parse the multi-part request for uploading an image.
-imageUpload.errorFormFieldMissing = The form did not contain a ''{0}'' field." 
+imageUpload.errorFormFieldMissing = The form did not contain a ''{0}'' field."
 					
 #
 # User Accounts pages
@@ -84,27 +84,27 @@ last_login = Last Login
 add_new_account = Add new account
 edit_account = Edit account
 external_auth_only = Externally Authenticated Only
-reset_password =  Reset password
+reset_password = Reset password
 reset_password_note = Note: Instructions for resetting the password will \
-                    be emailed to the address entered above. The password will not \
+be emailed to the address entered above. The password will not \
-                    be reset until the user follows the link provided in this email.
+be reset until the user follows the link provided in this email.
 new_password = New password
 confirm_password = Confirm new password
 minimum_password_length = Minimum of {0} characters in length.
 leave_password_unchanged = Leaving this blank means that the password will not be changed.
 confirm_initial_password = Confirm initial password
 
-new_account_1 = A new account for 
+new_account_1 = A new account for
 new_account_2 = was successfully created.
 new_account_title = new account
 new_account_notification = A notification email has been sent to {0} \
-                with instructions for activating the account and creating a password.
+with instructions for activating the account and creating a password.
 updated_account_1 = The account for
 updated_account_2 = has been updated.
 updated_account_title = updated account
 updated_account_notification = A confirmation email has been sent to {0} \
-                with instructions for resetting a password. \
+with instructions for resetting a password. \
-                The password will not be reset until the user follows the link provided in this email.
+The password will not be reset until the user follows the link provided in this email.
 deleted_accounts = Deleted {0} {0, choice, 0#accounts|1#account|1<accounts}.
 
 enter_new_password = Please enter your new password for {0}
@@ -126,8 +126,8 @@ view_all_accounts = View all accounts
 view_all_accounts_title = view all accounts
 
 new_account_note = Note: An email will be sent to the address entered above \
-                notifying that an account has been created. \
+notifying that an account has been created. \
-                It will include instructions for activating the account and creating a password.
+It will include instructions for activating the account and creating a password.
 
 initial_password = Initial password
 submit_add_new_account = Add new account
@@ -177,22 +177,22 @@ first_time_login = First time log in
 create_account = Create account
 
 cant_activate_while_logged_in = You may not activate the account for {0} while you are logged in as {1}. \
-                Please log out and try again.
+Please log out and try again.
 account_already_activated = The account for {0} has already been activated.
 
 cant_change_password_while_logged_in = You may not reset the password for {0} while you are logged in as {1}. \
-                Please log out and try again.
+Please log out and try again.
 password_change_not_pending = The password for {0} has already been reset.
 password_changed_subject = Password changed.
 account_no_longer_exists = The account you are trying to set a password on is no longer available. \
-                Please contact your system administrator if you think this is an error.
+Please contact your system administrator if you think this is an error.
 password_saved = Your password has been saved.
 password_saved_please_login	= Your password has been saved. Please log in.
 
 
 please_provide_contact_information = Please provide your contact information to finish creating your account.
 first_time_login_note = Note: An email will be sent to the address entered above notifying \
-                that an account has been created.
+that an account has been created.
 first_time_external_email_html = @@file files/accountFirstTimeExternal.html
 first_time_external_email_text = @@file files/accountFirstTimeExternal.txt
 
@@ -201,7 +201,7 @@ myAccount_confirm_changes = Your changes have been saved.
 myAccount_confirm_changes_plus_note = Your changes have been saved. A confirmation email has been sent to {0}.
 email_change_will_be_confirmed = Note: if email changes, a confirmation email will be sent to the new email address entered above.
 #email_changed_subject = "Your VIVO email account has been changed.");
-			
+
 who_can_edit_profile = Who can edit my profile
 add_profile_editor = Add profile editor
 select_existing_last_name = Select an existing last name
@@ -211,7 +211,6 @@ remove_selection_title = remove selection
 
 external_id_not_provided = Login failed - External ID is not found.
 external_id_already_in_use = User account already exists for ''{0}''
-logins_disabled_for_maintenance = User logins are temporarily disabled while the system is being maintained.
 
 error_no_email = You must supply an email address.
 error_email_already_exists = An account with that email address already exists.
@@ -220,20 +219,18 @@ error_external_auth_already_exists = An account with that external authorization
 error_no_first_name = You must supply a first name.
 error_no_last_name = You must supply a last name.
 error_no_role = You must select a role.
-error_no_password = No password supplied.
-error_password_length = Password must be between {0} and {1} characters.
 error_password_mismatch = Passwords do not match.
 
 logged_in_but_no_profile = You have logged in, but the system contains no profile for you.
 unknown_user_name = friend
-login_welcome_message = Welcome{1, choice, 1# |1< back}, {0} 
+login_welcome_message = Welcome{1, choice, 1# |1< back}, {0}
 external_login_failed = External login failed
 logged_out = You have logged out.
 
 insufficient_authorization = We're sorry, but you are not authorized to view the page you requested. If you think this is an error, please contact us and we'll be happy to help.
 
 #
-# "partial" individual templates ( /templates/freemarker/body/partials/individual ) 
+# "partial" individual templates ( /templates/freemarker/body/partials/individual )
 #
 manage_publications = manage publications
 manage_grants_and_projects = manage grants & projects
@@ -307,7 +304,7 @@ search_index_not_connected = The search index is not connected.
 failed = failed
 check_startup_status = Check startup status page and/or Tomcat logs for more information.
 search_indexer_idle = The search indexer is idle.
-most_recent_update = The most recent update was at 
+most_recent_update = The most recent update was at
 rebuild_button = Rebuild
 reset_search_index = Reset the search index and re-populate it.
 preparing_to_rebuild_index = Preparing to rebuild the search index.
@@ -322,7 +319,7 @@ warning = Warning
 warnings_issued = {0} issued warnings during startup.
 startup_trace = Startup trace
 full_list_startup = The full list of startup events and messages.
-startup_status = Startup Status
+startup_status = Startup status
 continue = Continue
 
 #
@@ -479,7 +476,7 @@ hide_show_properties = hide/show properties
 hide_properties = hide properties
 property_hierarchy = Property Hierarchy
 all_x_properties = All {0} Properties
-property_groups = Property Groups
+property_groups = Property groups
 add_new = Add new
 object = object
 data = data
@@ -496,7 +493,7 @@ object_property_hierarchy = Object property hierarchy
 data_property_hierarchy = Data property hierarchy
 
 site_config = Site Configuration
-internal_class = Institutional internal class
+internal_class_i_capped = Institutional internal class
 manage_profile_editing = Manage profile editing
 page_management = Page management
 menu_ordering_mixed_caps = Menu ordering
@@ -504,6 +501,18 @@ restrict_logins_mixed_caps = Restrict logins
 site_information = Site information
 user_accounts = User accounts
 
+#
+# search controller ( PagedSearchController.java )
+#
+error_in_search_request = The search request contained errors.
+enter_search_term = Please enter a search term.
+invalid_search_term = Search term was invalid
+paging_link_more = more...
+no_matching_results = No matching results.
+search_failed = Search failed.
+search_term_error_near = The search term had an error near
+search_for = Search for ''{0}''
+
 #
 # search templates ( /templates/freemarker/body/search )
 #
@@ -521,24 +530,12 @@ page_link = page link
 next_capitalized = Next
 
 #
-# search controller ( PagedSearchController.java )
+# shortview templates ( /templates/freemarker/body/partials/shortview )
-#
-error_in_search_request = The search request contained errors.
-enter_search_term = Please enter a search term.
-invalid_search_term = Search term was invalid
-paging_link_more = more...
-no_matching_results = No matching results.
-search_failed = Search failed.
-search_term_error_near = The search term had an error near
-search_for = Search for ''{0}''
-
-#
-# shortview templates ( /templates/freemarker/body/partials/shortview ) 
 #
 view_profile_page_for = View the profile page for
 
 #
-# menupage templates ( /templates/freemarker/body/partials/menupage ) 
+# menupage templates ( /templates/freemarker/body/partials/menupage )
 #
 browse_page_javascript_one = This browse page requires javascript, but your browser is set to disable javascript. Either enable javascript or use the
 browse_page_javascript_two = to browse for information.
@@ -552,14 +549,14 @@ browse_all_public_content = You can browse all of the public content currently i
 browse_all_content = browse all content
 
 #
-# partial templates ( /templates/freemarker/body/partials ) 
+# partial templates ( /templates/freemarker/body/partials )
 #
 no_content_create_groups_classes = There is currently no content in the system, or you need to create class groups and assign your classes to them.
 browse_capitalized = Browse
 browse_by = Browse by
 
 #
-# partial account templates ( /templates/freemarker/body/partials/accounts ) 
+# partial account templates ( /templates/freemarker/body/partials/accounts )
 #
 delete_button = Delete
 accounts = accounts
@@ -567,7 +564,7 @@ accounts_per_page = accounts per page
 update_button = Update
 
 #
-# pagemanagement templates ( /templates/freemarker/body/pagemanagement ) 
+# pagemanagement templates ( /templates/freemarker/body/pagemanagement )
 #
 title_capitalized = Title
 type_capitalized = Type
@@ -588,7 +585,7 @@ use_capitalized = Use
 to_order_menu_items = to set the order of menu items.
 
 #
-# menupage templates ( /templates/freemarker/body/menupage ) 
+# menupage templates ( /templates/freemarker/body/menupage )
 #
 page_not_configured = This page is not yet configured.
 implement_capitalized = Implement
@@ -599,10 +596,10 @@ no_html_specified = No HTML specified.
 page_text = page text
 
 sparql_query_results = Sparql Query Results
-no_results_returned = No results were returned. 
+no_results_returned = No results were returned.
 
 #
-# manage proxies templates ( /templates/freemarker/body/manageproxies ) 
+# manage proxies templates ( /templates/freemarker/body/manageproxies )
 #
 operation_successful = The operation was successful.
 operation_unsuccessful = The operation was unsuccessful. Full details can be found in the system log.
@@ -623,7 +620,7 @@ selected_profiles = Selected profiles
 save_profile_changes = Save changes to profiles
 
 #
-# page partials templates ( /templates/freemarker/page/partials ) 
+# page partials templates ( /templates/freemarker/page/partials )
 #
 copyright = copyright
 all_rights_reserved = All Rights Reserved.
@@ -650,7 +647,7 @@ menu_item = menu item
 version = Version
 
 #
-# widget templates ( /templates/freemarker/widgets ) 
+# widget templates ( /templates/freemarker/widgets )
 #
 individual_name = individual name
 vclassAlpha_not_implemented = vclassAlpha is not yet implemented.
@@ -668,11 +665,10 @@ account = account
 change_password_to_login = Change Password to Log in
 new_password_capitalized = New Password
 confirm_password_capitalized = Confirm Password
-minimum_password_length = Minimum of {0} characters in length.
 already_logged_in = You are already logged in.
 
 #
-# lib templates ( /templates/freemarker/lib ) 
+# lib templates ( /templates/freemarker/lib )
 #
 statistics = Statistics
 
@@ -695,7 +691,7 @@ add_label_for_language = Language
 unsupported_ie_version = This form is not supported in versions of Internet Explorer below version 8. Please upgrade your browser, or switch to another browser, such as FireFox.
 
 #
-# edit templates ( /templates/freemarker/edit and edit/forms ) 
+# edit templates ( /templates/freemarker/edit and edit/forms )
 #
 edit_capitalized = Edit
 add_capitalized = Add
@@ -764,7 +760,7 @@ label = label
 no_classes_to_select = There are no Classes in the system from which to select.
 
 #
-# vitro theme templates ( /themes/vitro/templates ) 
+# vitro theme templates ( /themes/vitro/templates )
 #
 powered_by = Powered by
 javascript_ie_alert_text = This site uses HTML elements that are not recognized by Internet Explorer 8 and below in the absence of JavaScript. As a result, the site will not be rendered appropriately. To correct this, please either enable JavaScript, upgrade to Internet Explorer 9, or use another browser.
@@ -780,7 +776,7 @@ search_vitro = Search VITRO
 filter_search = filter search
 
 #
-#  custom form javascript variables ( /templates/freemarker/edit/js) 
+# custom form javascript variables ( /templates/freemarker/edit/js)
 #
 select_an_existing = Select an existing
 or_create_new_one = or create a new one.
@@ -805,7 +801,7 @@ october = October
 november = November
 
 #
-#  miscellaneous javascript variables ( webapp/web/js) 
+# miscellaneous javascript variables ( webapp/web/js)
 #
 select_editor_and_profile = You must select a minimum of 1 editor and profile.
 

webapp/web/templates/freemarker/body/individual/individual-menu.ftl

@@ -18,7 +18,7 @@
     <#-- List the menu items -->
     <ul class="menuItems">
         <#list hasElement.statements as statement>
-            <li class="menuItem"><#include "${hasElement.template}"> <span class="controls"><!--p.editingLinks "hasElement" statement editable /--></span></li>
+            <li class="menuItem"><#include "${hasElement.template}"> <span class="controls"><!--p.editingLinks "hasElement" "" statement editable /--></span></li>
         </#list>
     </ul>
     

webapp/web/templates/freemarker/body/siteAdmin/siteAdmin-siteConfiguration.ftl

@@ -8,7 +8,7 @@
         
         <ul role="navigation">
             <#if siteConfig.internalClass?has_content>
-                <li role="listitem"><a href="${siteConfig.internalClass}" title="${i18n().internal_class}">${i18n().internal_class}</a></li>
+                <li role="listitem"><a href="${siteConfig.internalClass}" title="${i18n().internal_class}">${i18n().internal_class_i_capped}</a></li>
             </#if>     
             
             <#if siteConfig.manageProxies?has_content>

webapp/web/templates/freemarker/edit/forms/js/customFormWithAutocomplete.js

@@ -144,7 +144,7 @@ var customForm = {
         // Put this case first, because in edit mode with
         // validation errors we just want initFormFullView.
 //        if ((!this.supportEdit) && (this.editMode == 'edit' || this.editMode == 'repair')) {
-        if (this.editMode == 'edit' || this.editMode == 'repair') {
+        if (this.editMode == 'edit' || this.editMode == 'repair' || this.editMode == 'error') {
             this.initFormWithValidationErrors();
         }
         else if (this.findValidationErrors()) {
@@ -321,8 +321,12 @@ var customForm = {
                     },
                     complete: function(xhr, status) {
                         // Not sure why, but we need an explicit json parse here. 
-                        var results = $.parseJSON(xhr.responseText),                        
+                        var results = $.parseJSON(xhr.responseText);                        
-                            filteredResults = customForm.filterAcResults(results);
+                        var filteredResults = customForm.filterAcResults(results);
+                        
+                        if ( customForm.acTypes[$(selectedObj).attr('acGroupName')] == "http://www.w3.org/2004/02/skos/core#Concept" ) {
+                            filteredResults = customForm.removeConceptSubclasses(filteredResults);
+                        }
 
                         customForm.acCache[request.term] = filteredResults;
                         response(filteredResults);
@@ -423,6 +427,16 @@ var customForm = {
         
     },
         
+    removeConceptSubclasses: function(array) {
+       $(array).each(function(i) {
+          if(this["msType"] != "http://www.w3.org/2004/02/skos/core#Concept") {
+              //Remove from array
+              array.splice(i, 1);
+          }    
+       });
+       return array;
+    },
+
     showAutocompleteSelection: function(label, uri, selectedObj) {
         // hide the acSelector field and set it's value to the selected ac item
         this.hideFields($(selectedObj).parent());

webapp/web/templates/freemarker/lib/lib-properties.ftl

@@ -108,13 +108,13 @@ name will be used as the label. -->
     <#if editable>
         <#local url = property.addUrl>
         <#if url?has_content>
-            <@showAddLink property.localName label url />
+            <@showAddLink property.localName property.name label url />
         </#if>
     </#if>
 </#macro>
 
-<#macro showAddLink propertyLocalName label url>
+<#macro showAddLink propertyLocalName propertyName label url>
-    <#if propertyLocalName == "informationResourceInAuthorship" || propertyLocalName == "webpage" || propertyLocalName == "hasResearchArea">
+    <#if propertyName == "informationResourceInAuthorship" || propertyName == "webpage" || propertyLocalName == "hasResearchArea">
         <a class="add-${propertyLocalName}" href="${url}" title="${i18n().manage_list_of} ${label?lower_case}">
         <img class="add-individual" src="${urls.images}/individual/manage-icon.png" alt="${i18n().manage}" /></a>
     <#else>
@@ -131,30 +131,42 @@ name will be used as the label. -->
 <#macro propertyListItem property statement editable >
     <li role="listitem">    
         <#nested>       
-        <@editingLinks "${property.localName}" statement editable/>
+        <@editingLinks "${property.localName}" "${property.name}" statement editable/>
     </li>
 </#macro>
 
-<#macro editingLinks propertyLocalName statement editable>
+<#macro editingLinks propertyLocalName propertyName statement editable>
-    <#if editable && (propertyLocalName != "informationResourceInAuthorship" && propertyLocalName != "webpage" && propertyLocalName != "hasResearchArea")>
+    <#if editable && (propertyName != "authors" && propertyName != "webpage" && propertyLocalName != "hasResearchArea")>
-        <@editLink propertyLocalName statement />
+        <@editLink propertyLocalName propertyName statement />
-        <@deleteLink propertyLocalName statement />
+        <@deleteLink propertyLocalName propertyName statement />
      
     </#if>
 </#macro>
-
+<#macro editLink propertyLocalName propertyName statement>
-<#macro editLink propertyLocalName statement>
+<#if propertyLocalName?contains("ARG_2000028")>
+    <#if propertyName?contains("mailing address")>
+        <#local url = statement.editUrl + "&addressUri=" + "${statement.address!}">
+    <#elseif propertyName?contains("phone")>
+        <#local url = statement.editUrl + "&phoneUri=" + "${statement.phone!}">
+    <#elseif propertyName?contains("primary email") || propertyName?contains("additional emails")>
+        <#local url = statement.editUrl + "&emailUri=" + "${statement.email!}">
+    <#elseif propertyName?contains("full name")>
+        <#local url = statement.editUrl + "&fullNameUri=" + "${statement.fullName!}">
+    </#if>
+<#else>
     <#local url = statement.editUrl>
+</#if>
     <#if url?has_content>
         <@showEditLink propertyLocalName url />
     </#if>
+
 </#macro>
 
 <#macro showEditLink propertyLocalName url>
     <a class="edit-${propertyLocalName}" href="${url}" title="${i18n().edit_entry}"><img class="edit-individual" src="${urls.images}/individual/editIcon.gif" alt="${i18n().edit_entry}" /></a>
 </#macro>
 
-<#macro deleteLink propertyLocalName statement> 
+<#macro deleteLink propertyLocalName propertyName statement> 
     <#local url = statement.deleteUrl>
     <#if url?has_content>
         <@showDeleteLink propertyLocalName url />
@@ -197,7 +209,7 @@ name will be used as the label. -->
         <a href="${individual.imageUrl}" title="${i18n().alt_thumbnail_photo}">
         	<img class="individual-photo" src="${thumbUrl}" title="${i18n().click_to_view_larger}" alt="${individual.name}" width="${imageWidth!}" />
         </a>
-        <@editingLinks "${mainImage.localName}" mainImage.first() editable />
+        <@editingLinks "${mainImage.localName}" "" mainImage.first() editable />
     <#else>
         <#local imageLabel><@addLinkWithLabel mainImage editable "${i18n().photo}" /></#local>
         ${imageLabel}
@@ -218,7 +230,7 @@ name will be used as the label. -->
     <#local label = individual.nameStatement>
     ${label.value}
     <#if useEditLink>
-    	<@editingLinks "label" label editable />
+    	<@editingLinks "label" "" label editable />
     <#elseif editable || (labelCount > 1)>
     <#--We display the link even when the user is not logged in case of multiple labels-->
     	<#if editable>