Merge branch 'develop' into feature/theming

.gitignore

@@ -17,3 +17,8 @@ utilities/sdb_to_tdb/.work
 **/target
 
 **/overlays
+
+# Eclipse artifacts
+**/.settings
+**/.classpath
+**/.project

.travis.yml

@@ -1,13 +1,20 @@
 language: java
+dist: trusty
 sudo: false
 
 jdk:
+  - openjdk8
   - oraclejdk8
 
 env:
   # Give Maven 1GB of memory to work with
   - MAVEN_OPTS=-Xmx1024M
 
+cache:
+  directories:
+  - .autoconf
+  - $HOME/.m2
+
 install:
   - "echo 'Skipping install stage, dependencies will be downloaded during build and test stages.'"
 

api/pom.xml

@@ -7,13 +7,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vitro-api</artifactId>
-    <version>1.9.0-SNAPSHOT</version>
+    <version>1.10.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vitro-project</artifactId>
-        <version>1.9.0-SNAPSHOT</version>
+        <version>1.10.0-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -39,7 +39,7 @@
         <dependency>
             <groupId>org.vivoweb</groupId>
             <artifactId>vitro-dependencies</artifactId>
-            <version>1.9.0-SNAPSHOT</version>
+            <version>1.10.0-SNAPSHOT</version>
             <type>pom</type>
         </dependency>
         <dependency>

api/src/main/java/edu/cornell/mannlib/semservices/bo/BaseObject.java

@@ -0,0 +1,25 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+package edu.cornell.mannlib.semservices.bo;
+
+public class BaseObject {
+   /**
+    * Simple JavaBean domain object with an id property.
+    * Used as a base class for objects needing this property.
+    */
+   private Integer id;
+
+   public void setId(Integer id) {
+      this.id = id;
+   }
+
+   public Integer getId() {
+      return id;
+   }
+
+   public boolean isNew() {
+      return (this.id == null);
+   }
+
+
+
+}

api/src/main/java/edu/cornell/mannlib/semservices/bo/Concept.java

@@ -0,0 +1,163 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.semservices.bo;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class Concept {
+
+   private String definedBy;
+   private String conceptId;
+   private String bestMatch;
+   private String label;
+   private String type;
+   private String definition;
+   private String uri;
+   private String schemeURI;
+   private List<String> broaderURIList;
+   private List<String> narrowerURIList;
+   private List<String> exactMatchURIList;
+   private List<String> closeMatchURIList;
+   private List<String> altLabelList;
+   
+   /**
+    * default constructor
+    */
+   public Concept() {
+      this.broaderURIList = new ArrayList<String>();
+      this.narrowerURIList = new ArrayList<String>();
+      this.exactMatchURIList = new ArrayList<String>();
+      this.closeMatchURIList = new ArrayList<String>();
+   }
+   
+   /**
+    * @return the conceptId
+    */
+   public String getConceptId() {
+      return conceptId;
+   }
+   /**
+    * @param conceptId the conceptId to set
+    */
+   public void setConceptId(String conceptId) {
+      this.conceptId = conceptId;
+   }
+   /**
+    * @return the label
+    */
+   public String getLabel() {
+      return label;
+   }
+   /**
+    * @param label the label to set
+    */
+   public void setLabel(String label) {
+      this.label = label;
+   }
+   /**
+    * @return the type
+    */
+   public String getType() {
+      return type;
+   }
+   /**
+    * @param type the type to set
+    */
+   public void setType(String type) {
+      this.type = type;
+   }
+   /**
+    * @return the definition
+    */
+   public String getDefinition() {
+      return definition;
+   }
+   /**
+    * @param definition the definition to set
+    */
+   public void setDefinition(String definition) {
+      this.definition = definition;
+   }
+   /**
+    * @return the uri
+    */
+   public String getUri() {
+      return uri;
+   }
+   /**
+    * @param uri the uri to set
+    */
+   public void setUri(String uri) {
+      this.uri = uri;
+   }
+   /**
+    * @return the definedBy
+    */
+   public String getDefinedBy() {
+      return definedBy;
+   }
+   /**
+    * @param definedBy the definedBy to set
+    */
+   public void setDefinedBy(String definedBy) {
+      this.definedBy = definedBy;
+   }
+   /**
+    * @return the schemeURI
+    */
+   public String getSchemeURI() {
+      return schemeURI;
+   }
+   /**
+    * @param schemeURI the schemeURI to set
+    */
+   public void setSchemeURI(String schemeURI) {
+      this.schemeURI = schemeURI;
+   }
+   /**
+    * @return the bestMatch
+    */
+   public String getBestMatch() {
+      return bestMatch;
+   }
+   /**
+    * @param bestMatch the bestMatch to set
+    */
+   public void setBestMatch(String bestMatch) {
+      this.bestMatch = bestMatch;
+   }
+public List<String> getBroaderURIList() {
+	return broaderURIList;
+}
+public void setBroaderURIList(List<String> broaderURIList) {
+	this.broaderURIList = broaderURIList;
+}
+public List<String> getNarrowerURIList() {
+	return narrowerURIList;
+}
+public void setNarrowerURIList(List<String> narrowerURIList) {
+	this.narrowerURIList = narrowerURIList;
+}
+public List<String> getExactMatchURIList() {
+	return exactMatchURIList;
+}
+public void setExactMatchURIList(List<String> exactMatchURIList) {
+	this.exactMatchURIList = exactMatchURIList;
+}
+public List<String> getCloseMatchURIList() {
+	return closeMatchURIList;
+}
+public void setCloseMatchURIList(List<String> closeMatchURIList) {
+	this.closeMatchURIList = closeMatchURIList;
+}
+
+public List<String> getAltLabelList() {
+	return altLabelList;
+}
+
+public void setAltLabelList(List<String> altLabelList) {
+	this.altLabelList = altLabelList;
+}
+
+}

api/src/main/java/edu/cornell/mannlib/semservices/bo/ConceptInfo.java

@@ -0,0 +1,32 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.semservices.bo;
+
+
+import java.util.List;
+
+
+public class ConceptInfo extends SemanticServicesInfoBase {
+
+    private List<?> conceptList;
+    /**
+     *
+     */
+    public ConceptInfo() {
+        super();
+    }
+
+    /**
+     * @return the conceptList
+     */
+    public List<?> getConceptList() {
+        return conceptList;
+    }
+
+    /**
+     * @param conceptList the conceptList to set
+     */
+    public void setConceptList(List<?> conceptList) {
+        this.conceptList = conceptList;
+    }
+}

api/src/main/java/edu/cornell/mannlib/semservices/bo/SemanticServicesError.java

@@ -0,0 +1,75 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.semservices.bo;
+
+public class SemanticServicesError {
+   private String message;
+   private String exception;
+   private String severity;
+
+   /**
+    *
+    */
+   public SemanticServicesError() {
+      super();
+   }
+
+
+
+   /**
+    * @param exception Exception description
+    * @param message Error message
+    * @param severity Severity
+    */
+   public SemanticServicesError(String exception, String message, String severity) {
+      super();
+      this.exception = exception;
+      this.message = message;
+      this.severity = severity;
+   }
+
+
+
+   /**
+    * @return the message
+    */
+   public String getMessage() {
+      return message;
+   }
+
+   /**
+    * @param message the message to set
+    */
+   public void setMessage(String message) {
+      this.message = message;
+   }
+
+   /**
+    * @return the exception
+    */
+   public String getException() {
+      return exception;
+   }
+
+   /**
+    * @param exception the exception to set
+    */
+   public void setException(String exception) {
+      this.exception = exception;
+   }
+
+   /**
+    * @return the severity
+    */
+   public String getSeverity() {
+      return severity;
+   }
+
+   /**
+    * @param severity the severity to set
+    */
+   public void setSeverity(String severity) {
+      this.severity = severity;
+   }
+
+}

api/src/main/java/edu/cornell/mannlib/semservices/bo/SemanticServicesInfoBase.java

@@ -0,0 +1,29 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.semservices.bo;
+
+public class SemanticServicesInfoBase {
+
+   private SemanticServicesError semanticServicesError;
+   /**
+    *
+    */
+   public SemanticServicesInfoBase() {
+      super();
+      // TODO Auto-generated constructor stub
+   }
+
+   /**
+    * @return the semanticServicesError
+    */
+   public SemanticServicesError getSemanticServicesError() {
+      return semanticServicesError;
+   }
+   /**
+    * @param semanticServicesError the semanticServicesError to set
+    */
+   public void setSemanticServicesError(SemanticServicesError semanticServicesError) {
+      this.semanticServicesError = semanticServicesError;
+   }
+
+}

api/src/main/java/edu/cornell/mannlib/semservices/exceptions/ConceptsNotFoundException.java

@@ -0,0 +1,15 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.semservices.exceptions;
+
+public class ConceptsNotFoundException extends Exception {
+   /**
+    * An exception that indicates a service could not find a Concept
+    */
+   private static final long serialVersionUID = -4729465393290022840L;
+   public ConceptsNotFoundException() { }
+   public ConceptsNotFoundException(String message) { super(message); }
+   public ConceptsNotFoundException(Throwable cause) { super(cause); }
+   public ConceptsNotFoundException(String message, Throwable cause) { super(message, cause); }
+
+}

api/src/main/java/edu/cornell/mannlib/semservices/service/ExternalConceptService.java

@@ -0,0 +1,27 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.semservices.service;
+
+import java.util.List;
+
+import edu.cornell.mannlib.semservices.bo.Concept;
+
+public interface ExternalConceptService {
+
+	/**
+	 * @param term Term
+	 */
+	List<Concept> processResults(String term) throws Exception;
+
+	/**
+	 * @param term Term
+	 * @throws Exception
+	 */
+	List<Concept> getConcepts(String term) throws Exception;
+
+	/**
+	 * @param uri URI
+	 */
+	List<Concept> getConceptsByURIWithSparql(String uri) throws Exception;
+
+}

api/src/main/java/edu/cornell/mannlib/semservices/util/MetadataNamespaceContext.java

@@ -0,0 +1,26 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.semservices.util;
+import java.util.Iterator;
+import javax.xml.XMLConstants;
+import javax.xml.namespace.NamespaceContext;
+
+public class MetadataNamespaceContext implements NamespaceContext {
+    public String getNamespaceURI(String prefix) {
+        if (prefix == null) throw new NullPointerException("Null prefix");
+        else if ("mix".equals(prefix)) return "http://www.loc.gov/mix/";
+        else if ("xml".equals(prefix)) return XMLConstants.XML_NS_URI;
+        return XMLConstants.NULL_NS_URI;
+    }
+
+    // This method isn't necessary for XPath processing.
+    public String getPrefix(String uri) {
+        throw new UnsupportedOperationException();
+    }
+
+    // This method isn't necessary for XPath processing either.
+    public Iterator getPrefixes(String uri) {
+        throw new UnsupportedOperationException();
+    }
+
+}

api/src/main/java/edu/cornell/mannlib/semservices/util/SKOSUtils.java

@@ -0,0 +1,266 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+/* We are no longer using the SKOS API since Vitro has moved to V 4.0 of OWL API which does not appear to be compatible.
+ This file will contain methods used for reading SKOS as XML and parsing it for the properties
+ we want to extract*/
+
+package edu.cornell.mannlib.semservices.util;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.NodeIterator;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
+
+import edu.cornell.mannlib.semservices.bo.Concept;
+
+public class SKOSUtils {
+	protected final static Log log = LogFactory.getLog(SKOSUtils.class);
+
+	public static String getConceptXML(String conceptUriString) {
+		URL conceptURL = null;
+		try {
+			conceptURL = new URL(conceptUriString);
+		} catch (Exception e) {
+			log.error("Exception occurred in instantiating URL for "
+					+ conceptUriString, e);
+			// If the url is having trouble, just return null for the concept
+			return null;
+		}
+		log.debug("loading concept uri " + conceptUriString);
+
+		String results = null;
+		try {
+
+			StringWriter sw = new StringWriter();
+
+			BufferedReader in = new BufferedReader(new InputStreamReader(
+					conceptURL.openStream()));
+			String inputLine;
+			while ((inputLine = in.readLine()) != null) {
+				sw.write(inputLine);
+			}
+			in.close();
+
+			results = sw.toString();
+			log.debug(results);
+		} catch (Exception ex) {
+			log.error("Error occurred in getting concept from the URL "
+					+ conceptUriString, ex);
+			return null;
+		}
+		return results;
+	}
+
+	// Downloading the XML from the URI itself
+	// No language tag support here but can be specified if need be at this
+	// level as well
+	public static Concept createConceptUsingXMLFromURL(Concept concept,
+			String conceptURLString, String langTagValue, boolean addNotes) {
+		String results = getConceptXML(conceptURLString);
+		if (StringUtils.isEmpty(results)) {
+			return null;
+		}
+
+		// return createConceptUsingXML(concept, results, langTagValue);
+		return createConceptUsingXMLModel(concept, results, langTagValue,
+				addNotes);
+
+	}
+
+	// Because of the fact the xml returns matches by tag name, and the XML may
+	// look like <skos:narrower><skos:Concept ..><skos:broader
+	// rdf:resource:"conceptURI">
+	// where conceptURI is the concept that is the subject of skos:narrower, we
+	// need to ensure we are not returning the same uri as that of the main
+	// concept
+	public static List<String> removeConceptURIFromList(List<String> uris,
+			String conceptURI) {
+		// remove will return a boolean if the value exists in the list and is
+		// removed
+		// if/when it returns false, the URI is not in the list
+		while (uris.remove(conceptURI)) {
+		}
+		;
+		return uris;
+	}
+
+	/**
+	 * The above code, although functional, does not take advantage of the fact
+	 * that we can actually read and query the RDF in precisely the manner we
+	 * wish.
+	 */
+
+	public static Concept createConceptUsingXMLModel(Concept concept,
+			String results, String langTagValue, boolean addNotes) {
+
+		try {
+			String conceptURI = concept.getUri();
+
+			// Load Model from RDF
+			StringReader reader = new StringReader(results);
+			Model model = ModelFactory.createDefaultModel();
+			model.read(reader, null, "RDF/XML");
+
+			// Execute the following query to get the information we want for
+			// this resource
+
+			// Preferred label
+			List<String> labelLiterals = getPrefLabelsFromModel(conceptURI,
+					model, langTagValue);
+			if (labelLiterals.size() > 0) {
+				concept.setLabel(labelLiterals.get(0));
+			} else {
+				// This is an error because there should be at least one label
+				// returned
+				log.debug("The number of preferred labels is not greater than zero");
+			}
+
+			// Alternate label
+
+			List<String> altLabelList = getAltLabelsFromModel(conceptURI,
+					model, langTagValue);
+			concept.setAltLabelList(altLabelList);
+
+			// Broder, narrower, exact match, and close match properties
+
+			List<String> broaderURIList = getBroaderURIsFromModel(conceptURI,
+					model);
+			// broaderURIList = removeConceptURIFromList(broaderURIList,
+			// conceptURI);
+			concept.setBroaderURIList(broaderURIList);
+			List<String> narrowerURIList = getNarrowerURIsFromModel(conceptURI,
+					model);
+			// narrowerURIList = removeConceptURIFromList(narrowerURIList,
+			// conceptURI);
+			concept.setNarrowerURIList(narrowerURIList);
+
+			List<String> exactMatchURIList = getExactMatchURIsFromModel(
+					conceptURI, model);
+			// exactMatchURIList = removeConceptURIFromList(exactMatchURIList,
+			// conceptURI);
+			concept.setExactMatchURIList(exactMatchURIList);
+			List<String> closeMatchURIList = getCloseMatchURIsFromModel(
+					conceptURI, model);
+			// closeMatchURIList = removeConceptURIFromList(closeMatchURIList,
+			// conceptURI);
+			concept.setCloseMatchURIList(closeMatchURIList);
+
+			// Notes may exist, in which case they should be employed
+			if (addNotes) {
+				List<String> notes = getNotesFromModel(conceptURI, model,
+						langTagValue);
+				if (notes.size() > 0) {
+					concept.setDefinition(notes.get(0));
+				}
+			}
+
+		} catch (Exception e) {
+			log.error("error occurred in parsing " + results, e);
+		}
+
+		return concept;
+
+	}
+
+	private static List<String> getPrefLabelsFromModel(String conceptURI,
+			Model model, String langTagValue) {
+		String propertyURI = "http://www.w3.org/2004/02/skos/core#prefLabel";
+		return getLabelsFromModel(conceptURI, propertyURI, model, langTagValue);
+	}
+
+	private static List<String> getAltLabelsFromModel(String conceptURI,
+			Model model, String langTagValue) {
+		String propertyURI = "http://www.w3.org/2004/02/skos/core#altLabel";
+		return getLabelsFromModel(conceptURI, propertyURI, model, langTagValue);
+	}
+
+	private static List<String> getLabelsFromModel(String conceptURI,
+			String propertyURI, Model model, String langTagValue) {
+		List<String> labels = new ArrayList<String>();
+		StmtIterator statements = model.listStatements(
+				ResourceFactory.createResource(conceptURI),
+				ResourceFactory.createProperty(propertyURI), (RDFNode) null);
+		while (statements.hasNext()) {
+			Statement statement = statements.nextStatement();
+			RDFNode node = statement.getObject();
+			if (node != null && node.isLiteral()) {
+				String label = node.asLiteral().getString();
+				if (StringUtils.isNotEmpty(langTagValue)) {
+					String language = node.asLiteral().getLanguage();
+					if (language != null && language.equals(langTagValue)) {
+						labels.add(label);
+					}
+				} else {
+					labels.add(label);
+				}
+			}
+
+		}
+		return labels;
+	}
+
+	private static List<String> getNotesFromModel(String conceptURI,
+			Model model, String langTagValue) {
+		String propertyURI = "http://www.w3.org/2004/02/skos/core#note";
+		return getLabelsFromModel(conceptURI, propertyURI, model, langTagValue);
+	}
+
+	private static List<String> getCloseMatchURIsFromModel(String conceptURI,
+			Model model) {
+		String propertyURI = "http://www.w3.org/2004/02/skos/core#closeMatch";
+		return getRelatedURIsFromModel(conceptURI, propertyURI, model);
+
+	}
+
+	private static List<String> getExactMatchURIsFromModel(String conceptURI,
+			Model model) {
+		String propertyURI = "http://www.w3.org/2004/02/skos/core#exactMatch";
+		return getRelatedURIsFromModel(conceptURI, propertyURI, model);
+	}
+
+	private static List<String> getNarrowerURIsFromModel(String conceptURI,
+			Model model) {
+		String propertyURI = "http://www.w3.org/2004/02/skos/core#narrower";
+		return getRelatedURIsFromModel(conceptURI, propertyURI, model);
+	}
+
+	private static List<String> getBroaderURIsFromModel(String conceptURI,
+			Model model) {
+		String propertyURI = "http://www.w3.org/2004/02/skos/core#broader";
+		return getRelatedURIsFromModel(conceptURI, propertyURI, model);
+	}
+
+	private static List<String> getRelatedURIsFromModel(String conceptURI,
+			String propertyURI, Model model) {
+		List<String> URIs = new ArrayList<String>();
+		NodeIterator nodeIterator = model.listObjectsOfProperty(
+				ResourceFactory.createResource(conceptURI),
+				ResourceFactory.createProperty(propertyURI));
+
+		while (nodeIterator.hasNext()) {
+			RDFNode node = nodeIterator.nextNode();
+			if (node.isResource() && node.asResource().getURI() != null) {
+				String URI = node.asResource().getURI();
+				URIs.add(URI);
+			}
+		}
+
+		return URIs;
+	}
+
+}

api/src/main/java/edu/cornell/mannlib/semservices/util/XMLUtils.java

@@ -0,0 +1,361 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.semservices.util;
+
+import java.io.BufferedWriter;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStreamWriter;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.Writer;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Source;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.TransformerFactoryConfigurationError;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpressionException;
+import javax.xml.xpath.XPathFactory;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.DocumentType;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+/**
+ * Convenience Class to parse XML strings to DOM Document for XML contents
+ * retrieval.
+ */
+public class XMLUtils {
+    private static DocumentBuilder parser;
+    public static Writer writer;
+    static private String indent = "";
+    protected static final Log logger = LogFactory.getLog(XMLUtils.class);
+
+
+    /**
+     * @throws ParserConfigurationException
+     */
+    public static DocumentBuilder getDocumentBuilder()
+            throws ParserConfigurationException {
+        if (parser == null) {
+            // JPT: Remove xerces use
+            DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory
+                    .newInstance();
+            documentBuilderFactory.setNamespaceAware(true);
+            documentBuilderFactory.setValidating(false);
+            parser = documentBuilderFactory.newDocumentBuilder();
+        }
+
+        return parser;
+    }
+
+    /**
+     * @param xmlString XML String
+     * @throws IOException
+     * @throws SAXException
+     * @throws ParserConfigurationException
+     */
+    public synchronized static Document parse(String xmlString)
+            throws IOException, SAXException, ParserConfigurationException {
+        StringReader reader = new StringReader(xmlString);
+        InputSource inputSource = new InputSource(reader);
+        return getDocumentBuilder().parse(inputSource);
+    }
+
+    /**
+     * @param stream Input stream
+     * @throws IOException
+     * @throws SAXException
+     * @throws ParserConfigurationException
+     */
+    public synchronized static Document parse(InputStream stream)
+            throws IOException, SAXException, ParserConfigurationException {
+        return getDocumentBuilder().parse(stream);
+    }
+
+    /**
+     * @param document DOM Document
+     * @param name Name
+     */
+    public static String getElementByName(Document document, String name) {
+        NodeList nodes = document.getElementsByTagName(name);
+        String s = null;
+        for (int i=0; i < nodes.getLength() ; i++) {
+            Node node = nodes.item(i);
+            s = node.getTextContent().trim();
+        }
+        return s;
+    }
+
+    /**
+    * @param doc DOM Document
+    * @throws IOException
+    */
+    @SuppressWarnings("deprecation")
+   public static void serializeDoc(Document doc) throws IOException {
+       org.apache.xml.serialize.XMLSerializer serializer = new org.apache.xml.serialize.XMLSerializer();
+       serializer.setOutputByteStream(System.out);
+       serializer.serialize(doc);
+    }
+
+   @SuppressWarnings("deprecation")
+   public static String serializeDoctoString(Document doc) throws IOException {
+	   org.apache.xml.serialize.XMLSerializer serializer = new org.apache.xml.serialize.XMLSerializer();
+      ByteArrayOutputStream bout = new ByteArrayOutputStream();
+
+      serializer.setOutputByteStream(bout);
+      serializer.serialize(doc);
+      return bout.toString();
+   }
+
+    /**
+    * @param xml XML String
+    */
+   public static void prettyPrint(String xml) {
+       Source xmlInput = new StreamSource(new StringReader(xml));
+       StreamResult xmlOutput = new StreamResult(new StringWriter());
+       Transformer transformer = null;
+      try {
+         transformer = TransformerFactory.newInstance().newTransformer();
+      } catch (TransformerConfigurationException e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      } catch (TransformerFactoryConfigurationError e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      }
+       //transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "testing.dtd");
+       transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+       transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
+       try {
+         transformer.transform(xmlInput, xmlOutput);
+      } catch (TransformerException e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      }
+       String formattedxml=xmlOutput.getWriter().toString();
+       System.out.println(formattedxml);
+
+    }
+
+   /**
+    * @param xml XML String
+    */
+   public static String prettyPrintToString(String xml) {
+       Source xmlInput = new StreamSource(new StringReader(xml));
+       StreamResult xmlOutput = new StreamResult(new StringWriter());
+       Transformer transformer = null;
+      try {
+         transformer = TransformerFactory.newInstance().newTransformer();
+      } catch (TransformerConfigurationException e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      } catch (TransformerFactoryConfigurationError e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      }
+       //transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "testing.dtd");
+       transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+       transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
+       try {
+         transformer.transform(xmlInput, xmlOutput);
+      } catch (TransformerException e) {
+         // TODO Auto-generated catch block
+         e.printStackTrace();
+      }
+       String formattedxml=xmlOutput.getWriter().toString();
+       return formattedxml;
+
+    }
+
+    /**
+    * @param node DOM Node
+    */
+   public static void displayNodeInfo(Node node) {
+       switch (node.getNodeType()) {
+       case Node.DOCUMENT_NODE:
+         System.out.println("Document Node ");
+         break;
+       case Node.ELEMENT_NODE:
+         System.out.println("Element Node: "+ node.getNodeName());
+         break;
+       case Node.TEXT_NODE:
+         System.out.println("Text Node: "+ node.getNodeName());
+         break;
+       case Node.CDATA_SECTION_NODE:
+         System.out.println("CDATA Section Node: ");
+         break;
+       case Node.COMMENT_NODE:
+         System.out.println("Comment Node ");
+         break;
+       case Node.PROCESSING_INSTRUCTION_NODE:
+         System.out.println("Processing Instruction Node ");
+         break;
+       case Node.ENTITY_REFERENCE_NODE:
+         System.out.println("Entity Reference Node ");
+         break;
+       case Node.DOCUMENT_TYPE_NODE:
+         System.out.println("Document Type Node ");
+         break;
+       }
+    }
+
+    /**
+    * @param node DOM Node
+    * @throws IOException
+    */
+   public static void serializeNode(Node node) throws IOException {
+       if (writer == null) writer = new BufferedWriter(new OutputStreamWriter(System.out));
+
+       switch (node.getNodeType()) {
+       case Node.DOCUMENT_NODE:
+         Document doc = (Document) node;
+         writer.write("<?xml version=\"");
+         writer.write(doc.getXmlVersion());
+         writer.write("\" encoding=\"UTF-8\" standalone=\"");
+         if (doc.getXmlStandalone())
+           writer.write("yes");
+         else
+           writer.write("no");
+         writer.write("\"?>\n");
+
+         NodeList nodes = node.getChildNodes();
+         if (nodes != null)
+           for (int i = 0; i < nodes.getLength(); i++)
+             serializeNode(nodes.item(i));
+         break;
+       case Node.ELEMENT_NODE:
+         String name = node.getNodeName();
+         writer.write("<" + name);
+         NamedNodeMap attributes = node.getAttributes();
+         for (int i = 0; i < attributes.getLength(); i++) {
+           Node current = attributes.item(i);
+           writer.write(" " + current.getNodeName() + "=\"");
+           print(current.getNodeValue());
+           writer.write("\"");
+         }
+         writer.write(">");
+
+         NodeList children = node.getChildNodes();
+         if (children != null) {
+           //if ((children.item(0) != null) && (children.item(0).getNodeType() == Node.ELEMENT_NODE))
+           //  writer.write("\n");
+
+           for (int i = 0; i < children.getLength(); i++)
+             serializeNode(children.item(i));
+           if ((children.item(0) != null)
+               && (children.item(children.getLength() - 1).getNodeType() == Node.ELEMENT_NODE))
+             writer.write("");
+         }
+
+         writer.write("</" + name + ">");
+         break;
+       case Node.TEXT_NODE:
+         print(node.getNodeValue());
+         break;
+       case Node.CDATA_SECTION_NODE:
+         writer.write("CDATA");
+         print(node.getNodeValue());
+         writer.write("");
+         break;
+       case Node.COMMENT_NODE:
+         writer.write("<!-- " + node.getNodeValue() + " -->\n");
+         break;
+       case Node.PROCESSING_INSTRUCTION_NODE:
+         writer.write("<?" + node.getNodeName() + " " + node.getNodeValue() + "?>\n");
+         break;
+       case Node.ENTITY_REFERENCE_NODE:
+         writer.write("&" + node.getNodeName() + ";");
+         break;
+       case Node.DOCUMENT_TYPE_NODE:
+         DocumentType docType = (DocumentType) node;
+         String publicId = docType.getPublicId();
+         String systemId = docType.getSystemId();
+         String internalSubset = docType.getInternalSubset();
+         writer.write("<!DOCTYPE " + docType.getName());
+         if (publicId != null)
+           writer.write(" PUBLIC \"" + publicId + "\" ");
+         else
+           writer.write(" SYSTEM ");
+         writer.write("\"" + systemId + "\"");
+         if (internalSubset != null)
+           writer.write(" [" + internalSubset + "]");
+         writer.write(">\n");
+         break;
+       }
+       writer.flush();
+     }
+
+    /**
+    * @param s String
+    * @throws IOException
+    */
+   private static void print(String s) throws IOException {
+       if (s == null)
+         return;
+       for (int i = 0, len = s.length(); i < len; i++) {
+         char c = s.charAt(i);
+         switch (c) {
+         case '<':
+           writer.write("&lt;");
+           break;
+         case '>':
+           writer.write("&gt;");
+           break;
+         case '&':
+           writer.write("&amp;");
+           break;
+         case '\r':
+           writer.write("&#xD;");
+           break;
+         default:
+           writer.write(c);
+         }
+       }
+     }
+
+    /**
+     * @param obj (either a Document or a Node)
+     * @param expression Expression
+     * @return string contents
+     */
+    public static Node getNodeWithXpath(Object obj, String expression) {
+       Object root = null;
+       if (obj instanceof Document) {
+          Document doc = (Document) obj;
+          root = doc.getDocumentElement();
+       } else {
+          root = (Node) obj;
+       }
+
+        XPath xpath = XPathFactory.newInstance().newXPath();
+        xpath.setNamespaceContext(new MetadataNamespaceContext());
+        Node result = null;
+
+        try {
+            result = ((Node) xpath.evaluate(expression, root, XPathConstants.NODE));
+            return result;
+        } catch (XPathExpressionException e) {
+            logger.error("XPathExpressionException ", e);
+            return null;
+        }
+    }
+
+}

api/src/main/java/edu/cornell/mannlib/vedit/tags/DynamicFieldsTag.java

@@ -27,7 +27,7 @@ import edu.cornell.mannlib.vedit.beans.FormObject;
 import edu.cornell.mannlib.vedit.beans.DynamicField;
 import edu.cornell.mannlib.vedit.beans.DynamicFieldRow;
 import org.apache.commons.codec.binary.Base64;
-import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
 import edu.cornell.mannlib.vedit.tags.EditTag;
 
 public class DynamicFieldsTag extends EditTag {

api/src/main/java/edu/cornell/mannlib/vedit/tags/EditTag.java

@@ -11,7 +11,7 @@ import javax.servlet.jsp.JspWriter;
 
 import edu.cornell.mannlib.vedit.beans.EditProcessObject;
 import edu.cornell.mannlib.vedit.beans.FormObject;
-import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
 
 public class EditTag extends TagSupport {
     private String name = null;

api/src/main/java/edu/cornell/mannlib/vedit/tags/ErrorTag.java

@@ -7,7 +7,7 @@ import javax.servlet.jsp.tagext.TagSupport;
 import javax.servlet.jsp.JspWriter;
 import edu.cornell.mannlib.vedit.beans.FormObject;
 import edu.cornell.mannlib.vedit.tags.EditTag;
-import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
 
 /** This tag allows validation error messages to be displayed on a form JSP **/
 public class ErrorTag extends EditTag {
@@ -29,7 +29,7 @@ public class ErrorTag extends EditTag {
             }
 
             if (errors != null){
-                out.print(StringEscapeUtils.escapeHtml((String) errors));
+                out.print(StringEscapeUtils.ESCAPE_HTML4.translate((String) errors));
             }
 
         } catch(Exception ex) {

api/src/main/java/edu/cornell/mannlib/vedit/tags/OptionTag.java

@@ -12,7 +12,7 @@ import javax.servlet.jsp.JspWriter;
 
 import edu.cornell.mannlib.vedit.beans.Option;
 import edu.cornell.mannlib.vedit.tags.EditTag;
-import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
 
 public class OptionTag extends EditTag {
     private String name = null;
@@ -29,11 +29,11 @@ public class OptionTag extends EditTag {
                 opt.setValue("");
             if (opt.getBody() == null)
                 opt.setBody("");
-            out.print("<option value=\""+StringEscapeUtils.escapeHtml(opt.getValue())+"\"");
+            out.print("<option value=\""+StringEscapeUtils.ESCAPE_HTML4.translate(opt.getValue())+"\"");
             if (opt.getSelected())
                 out.print(" selected=\"selected\"");
             out.print(">");
-            out.print(StringEscapeUtils.escapeHtml(opt.getBody()));
+            out.print(StringEscapeUtils.ESCAPE_HTML4.translate(opt.getBody()));
             out.print("</option>\n");
         }
     }
@@ -54,7 +54,7 @@ public class OptionTag extends EditTag {
                 OrderedMapIterator ogKey = optGroups.orderedMapIterator();
                 while (ogKey.hasNext()) {
                     String optGroupName = (String) ogKey.next();
-                    out.println("<optgroup label=\""+StringEscapeUtils.escapeHtml(optGroupName)+"\">");
+                    out.println("<optgroup label=\""+StringEscapeUtils.ESCAPE_HTML4.translate(optGroupName)+"\">");
                     outputOptionsMarkup((List)optGroups.get(optGroupName),out);
                     out.println("</optgroup>");
                 }

api/src/main/java/edu/cornell/mannlib/vedit/tags/ValueTag.java

@@ -8,7 +8,7 @@ import javax.servlet.jsp.JspException;
 import javax.servlet.jsp.tagext.TagSupport;
 import javax.servlet.jsp.JspWriter;
 import edu.cornell.mannlib.vedit.beans.FormObject;
-import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
 import edu.cornell.mannlib.vedit.tags.EditTag;
 
 public class ValueTag extends EditTag {
@@ -35,7 +35,7 @@ public class ValueTag extends EditTag {
             if (values != null){
                 String value = (String) values.get(name);
                 if (value != null)
-                    out.print(StringEscapeUtils.escapeHtml(value));
+                    out.print(StringEscapeUtils.ESCAPE_HTML4.translate(value));
             } else {
                 System.out.println("ValueTag unable to get HashMap of form values");
             }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/ApplicationImpl.java

@@ -25,7 +25,6 @@ import edu.cornell.mannlib.vitro.webapp.startup.ComponentStartupStatusImpl;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 import edu.cornell.mannlib.vitro.webapp.triplesource.impl.BasicCombinedTripleSource;
 import edu.cornell.mannlib.vitro.webapp.utils.configuration.Property;
-import edu.cornell.mannlib.vitro.webapp.utils.configuration.Validation;
 
 /**
  * The basic implementation of the Application interface.
@@ -69,15 +68,9 @@ public class ApplicationImpl implements Application {
 		return searchEngine;
 	}
 
-	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasSearchEngine")
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasSearchEngine", minOccurs = 1, maxOccurs = 1)
 	public void setSearchEngine(SearchEngine se) {
-		if (searchEngine == null) {
 		searchEngine = se;
-		} else {
-			throw new IllegalStateException(
-					"Configuration includes multiple SearchEngine instances: "
-							+ searchEngine + ", and " + se);
-		}
 	}
 
 	@Override
@@ -85,15 +78,9 @@ public class ApplicationImpl implements Application {
 		return searchIndexer;
 	}
 
-	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasSearchIndexer")
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasSearchIndexer", minOccurs = 1, maxOccurs = 1)
 	public void setSearchIndexer(SearchIndexer si) {
-		if (searchIndexer == null) {
 		searchIndexer = si;
-		} else {
-			throw new IllegalStateException(
-					"Configuration includes multiple SearchIndexer instances: "
-							+ searchIndexer + ", and " + si);
-		}
 	}
 
 	@Override
@@ -101,15 +88,9 @@ public class ApplicationImpl implements Application {
 		return imageProcessor;
 	}
 
-	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasImageProcessor")
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasImageProcessor", minOccurs = 1, maxOccurs = 1)
 	public void setImageProcessor(ImageProcessor ip) {
-		if (imageProcessor == null) {
 		imageProcessor = ip;
-		} else {
-			throw new IllegalStateException(
-					"Configuration includes multiple ImageProcessor instances: "
-							+ imageProcessor + ", and " + ip);
-		}
 	}
 
 	@Override
@@ -117,15 +98,9 @@ public class ApplicationImpl implements Application {
 		return fileStorage;
 	}
 
-	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasFileStorage")
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasFileStorage", minOccurs = 1, maxOccurs = 1)
 	public void setFileStorage(FileStorage fs) {
-		if (fileStorage == null) {
 		fileStorage = fs;
-		} else {
-			throw new IllegalStateException(
-					"Configuration includes multiple FileStorage instances: "
-							+ fileStorage + ", and " + fs);
-		}
 	}
 
 	@Override
@@ -133,15 +108,9 @@ public class ApplicationImpl implements Application {
 		return contentTripleSource;
 	}
 
-	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasContentTripleSource")
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasContentTripleSource", minOccurs = 1, maxOccurs = 1)
 	public void setContentTripleSource(ContentTripleSource source) {
-		if (contentTripleSource == null) {
 		contentTripleSource = source;
-		} else {
-			throw new IllegalStateException(
-					"Configuration includes multiple instances of ContentTripleSource: "
-							+ contentTripleSource + ", and " + source);
-		}
 	}
 
 	@Override
@@ -149,15 +118,9 @@ public class ApplicationImpl implements Application {
 		return configurationTripleSource;
 	}
 
-	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasConfigurationTripleSource")
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasConfigurationTripleSource", minOccurs = 1, maxOccurs = 1)
 	public void setConfigurationTripleSource(ConfigurationTripleSource source) {
-		if (configurationTripleSource == null) {
 		configurationTripleSource = source;
-		} else {
-			throw new IllegalStateException(
-					"Configuration includes multiple instances of ConfigurationTripleSource: "
-							+ configurationTripleSource + ", and " + source);
-		}
 	}
 
 	@Override
@@ -165,47 +128,9 @@ public class ApplicationImpl implements Application {
 		return tboxReasonerModule;
 	}
 
-	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasTBoxReasonerModule")
+	@Property(uri = "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#hasTBoxReasonerModule", minOccurs = 1, maxOccurs = 1)
 	public void setTBoxReasonerModule(TBoxReasonerModule module) {
-		if (tboxReasonerModule == null) {
 		tboxReasonerModule = module;
-		} else {
-			throw new IllegalStateException(
-					"Configuration includes multiple instances of TBoxReasonerModule: "
-							+ tboxReasonerModule + ", and " + module);
-		}
-	}
-
-	@Validation
-	public void validate() throws Exception {
-		if (searchEngine == null) {
-			throw new IllegalStateException(
-					"Configuration did not include a SearchEngine.");
-		}
-		if (searchIndexer == null) {
-			throw new IllegalStateException(
-					"Configuration did not include a SearchIndexer.");
-		}
-		if (imageProcessor == null) {
-			throw new IllegalStateException(
-					"Configuration did not include an ImageProcessor.");
-		}
-		if (fileStorage == null) {
-			throw new IllegalStateException(
-					"Configuration did not include a FileStorage.");
-		}
-		if (contentTripleSource == null) {
-			throw new IllegalStateException(
-					"Configuration did not include a ContentTripleSource.");
-		}
-		if (configurationTripleSource == null) {
-			throw new IllegalStateException(
-					"Configuration did not include a ConfigurationTripleSource.");
-		}
-		if (tboxReasonerModule == null) {
-			throw new IllegalStateException(
-					"Configuration did not include a TBoxReasonerModule.");
-		}
 	}
 
 	@Override

api/src/main/java/edu/cornell/mannlib/vitro/webapp/auth/identifier/common/IsBlacklisted.java

@@ -12,7 +12,7 @@ import java.util.Set;
 
 import javax.servlet.ServletContext;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/config/ConfigurationPropertiesSmokeTests.java

@@ -10,7 +10,7 @@ import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/FedoraDatastreamController.java

@@ -1,713 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.controller;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.security.MessageDigest;
-import java.text.SimpleDateFormat;
-import java.util.List;
-import java.util.Properties;
-
-import javax.servlet.ServletContext;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import edu.cornell.mannlib.vitro.webapp.utils.JSPPageHandler;
-import org.apache.commons.fileupload.FileItem;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.joda.time.DateTime;
-
-import org.apache.jena.datatypes.xsd.XSDDatatype;
-import org.apache.jena.ontology.DatatypeProperty;
-import org.apache.jena.ontology.ObjectProperty;
-import org.apache.jena.ontology.OntModel;
-import org.apache.jena.rdf.model.Resource;
-import org.apache.jena.rdf.model.Statement;
-import org.apache.jena.vocabulary.RDFS;
-import org.apache.jena.vocabulary.XSD;
-import com.ibm.icu.util.Calendar;
-
-import edu.cornell.mannlib.vedit.beans.LoginStatusBean;
-import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
-import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
-import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
-import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
-import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
-import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
-import fedora.client.FedoraClient;
-import fedora.common.Constants;
-import fedora.server.management.FedoraAPIM;
-import fedora.server.types.gen.Datastream;
-
-
-/**
- * Handles a request to change a datastream in a fedora repository.
- * Some of this code is copied from N3MultiPartUpload.java
- * 
- * @author bdc34
- *
- */
-public class FedoraDatastreamController extends VitroHttpServlet implements Constants{
-    private static String FEDORA_PROPERTIES = "/WEB-INF/fedora.properties";
-    private static String DEFAULT_DSID = "DS1";
-    
-    private String fedoraUrl = null;
-    private String adminUser = null;
-    private String adminPassword = null;
-    private String pidNamespace = null;    
-    private String configurationStatus = "<p>Fedora configuration not yet loaded</p>";
-    private boolean configured = false;
-    private boolean connected = false;
-    
-    private static final int DEFAULT_MAX_SIZE = 1024 * 1024 * 50;//Shoudl this be changed to 1 GB to be consistent
-    private static final String DEFAULT_BASE_DIR = "/usr/local/vitrofiles";
-    private static String baseDirectoryForFiles = DEFAULT_BASE_DIR;
-    private static int maxFileSize = DEFAULT_MAX_SIZE;
-    
-    protected String contentTypeProperty = VitroVocabulary.CONTENT_TYPE;
-	protected String fileSizeProperty = VitroVocabulary.FILE_SIZE;
-    protected String fileNameProperty = VitroVocabulary.FILE_NAME;
-    protected String fileLocationProperty = VitroVocabulary.FILE_LOCATION;
-    protected String fileLabelProperty = RDFS.label.getURI();
-	protected String checksumNodeProperty = "";//Object property linking file to check sum node object
-	protected String checksumNodeDateTimeProperty = "";
-	protected String checksumNodeValueProperty = "";
-    protected String checksumDataProperty = ""; //is there a vitro equivalent?
-    
-    protected String deleteNs = "";
-    protected String individualPrefix = "";
-    protected String fedoraNs = VitroVocabulary.VITRO_FEDORA;
-    
-    
-    /**
-     * The get will present a form to the user. 
-     */
-    @Override
-	public void doGet(HttpServletRequest req, HttpServletResponse res)
-			throws IOException, ServletException {
-        try {
-            super.doGet(req, res);
-            log.debug("In doGet");
-            
-            VitroRequest vreq = new VitroRequest(req);
-    		OntModel sessionOntModel = ModelAccess.on(getServletContext()).getOntModel();
-            
-            synchronized (FedoraDatastreamController.class) {
-                if( fedoraUrl == null ){
-                    setup( sessionOntModel, getServletContext() );
-                    if( fedoraUrl == null ) 
-                        throw new FdcException("Connection to the file repository is " +
-                        		"not setup correctly.  Could not read fedora.properties file");
-                }else{
-                    if( !canConnectToFedoraServer() ){
-                        fedoraUrl = null;
-                        throw new FdcException("Could not connect to Fedora.");
-                    }                   
-                }
-            }     
-            FedoraClient fedora;
-            try { fedora = new FedoraClient(fedoraUrl,adminUser,adminPassword); } 
-            catch (MalformedURLException e) {
-                throw new FdcException("Malformed URL for fedora Repository location: " + fedoraUrl); 
-            }
-            
-            FedoraAPIM apim;
-            try { apim = fedora.getAPIM(); } catch (Exception e) {
-                throw new FdcException("could not create fedora APIM:" + e.getMessage());
-            }
-
-            //check if logged in
-                        
-            //get URI for file individual
-            if( req.getParameter("uri") == null || "".equals(req.getParameter("uri")))                                        
-                throw new FdcException("No file uri specified in request");
-            
-            boolean isDelete =  (req.getParameter("delete") != null && "true".equals(req.getParameter("delete")));
-           
-            String fileUri = req.getParameter("uri");
-            //check if file individual has a fedora:PID for a data stream                        
-            IndividualDao iwDao = vreq.getWebappDaoFactory().getIndividualDao();
-            Individual entity = iwDao.getIndividualByURI(fileUri);
-            
-
-            
-            if( entity == null )
-                throw new FdcException( "No entity found in system for file uri " + fileUri);
-            //System.out.println("Entity == null:" + (entity == null));                
-            //get the fedora PID
-            //System.out.println("entity data property " + entity.getDataPropertyMap().get(VitroVocabulary.FEDORA_PID));
-            if( entity.getDataPropertyMap().get(VitroVocabulary.FEDORA_PID ) == null )
-                throw new FdcException( "No fedora:pid found in system for file uri " + fileUri);            
-            List<DataPropertyStatement> stmts = entity.getDataPropertyMap().get(VitroVocabulary.FEDORA_PID).getDataPropertyStatements();
-            if( stmts == null || stmts.size() == 0)
-                throw new FdcException( "No fedora:pid found in system for file uri " + fileUri);
-            String pid = null;
-            for(DataPropertyStatement stmt : stmts){
-                if( stmt.getData() != null && stmt.getData().length() > 0){
-                    pid = stmt.getData();
-                    break;
-                }
-            }
-            //System.out.println("pid is " + pid + " and comparison is " + (pid == null));
-            if( pid == null )
-                throw new FdcException( "No fedora:pid found in system for file uri " + fileUri);
-            req.setAttribute("pid", pid);
-            req.setAttribute("fileUri", fileUri);
-          //get current file name to use on form
-            req.setAttribute("fileName", entity.getName());     
-            
-            if(isDelete)
-            {
-            	//Execute a 'deletion', i.e. unlink dataset and file, without removing file
-            	//Also save deletion as a deleteEvent entity which can later be queried
-            	
-            	 String datasetUri = null;
-                 //Get dataset uri by getting the fromDataSet property
-            	 edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty  fromDataSet = entity.getObjectPropertyMap().get(fedoraNs + "fromDataSet");
-            	 if(fromDataSet != null)
-            	 {
-	                 List<ObjectPropertyStatement> fromDsStmts = fromDataSet.getObjectPropertyStatements();
-	                 if(fromDsStmts.size() > 0) {
-	                 	datasetUri = fromDsStmts.get(0).getObjectURI();
-	                 	//System.out.println("object uri should be " + datasetUri);
-	                 } else {
-	                 	//System.out.println("No matching dataset uri could be found");
-	                 } 
-                 } else {
-                	 //System.out.println("From dataset is null");
-                 }
-            	 
-                 req.setAttribute("dataseturi", datasetUri);
-            	 boolean success = deleteFile(req, entity, iwDao, sessionOntModel);
-            	 req.setAttribute("deletesuccess", (success)?"success":"error");
-                 JSPPageHandler.renderBasicPage(req, res, "/edit/fileDeleteConfirm.jsp");
-            }
-            else{
-	            //check if the data stream exists in the fedora repository
-	            Datastream ds = apim.getDatastream(pid,DEFAULT_DSID,null);
-	            if( ds == null )
-	                throw new FdcException("There was no datastream in the " +
-	                		"repository for " + pid + " " + DEFAULT_DSID);            
-	            req.setAttribute("dsid", DEFAULT_DSID);
-	            
-	                   
-	            
-	            //forward to form     
-                JSPPageHandler.renderBasicPage(req, res, "/fileupload/datastreamModification.jsp");
-            }
-        }catch(FdcException ex){
-            req.setAttribute("errors", ex.getMessage());
-            JSPPageHandler.renderPlainPage(req, res, "/edit/fileUploadError.jsp");
-            return;
-        }
-    }
-                
-    @Override
-	public long maximumMultipartFileSize() {
-    	return maxFileSize;
-	}
-
-	@Override
-	public boolean stashFileSizeException() {
-		return true;
-	}
-
-	@Override
-	public void doPost(HttpServletRequest rawRequest, HttpServletResponse res)
-			throws ServletException, IOException {
-        try{
-        	VitroRequest req = new VitroRequest(rawRequest);
-        	if (req.hasFileSizeException()) {
-        		throw new FdcException("Size limit exceeded: " + req.getFileSizeException().getLocalizedMessage());
-        	}
-        	if (!req.isMultipart()) {
-        		throw new FdcException("Must POST a multipart encoded request");
-        	}
-        	
-            //check if fedora is on line
-    		OntModel sessionOntModel = ModelAccess.on(getServletContext()).getOntModel();
-            synchronized (FedoraDatastreamController.class) {
-                if( fedoraUrl == null ){
-                    setup( sessionOntModel, getServletContext() );
-                    if( fedoraUrl == null ) 
-                        throw new FdcException("Connection to the file repository is " +
-                                "not setup correctly.  Could not read fedora.properties file");
-                }else{
-                    if( !canConnectToFedoraServer() ){
-                        fedoraUrl = null;
-                        throw new FdcException("Could not connect to Fedora.");
-                    }                   
-                }
-            }     
-            FedoraClient fedora;
-            try { fedora = new FedoraClient(fedoraUrl,adminUser,adminPassword); } 
-            catch (MalformedURLException e) {
-                throw new FdcException("Malformed URL for fedora Repository location: " + fedoraUrl); 
-            }            
-            FedoraAPIM apim;
-            try { apim = fedora.getAPIM(); } catch (Exception e) {
-                throw new FdcException("could not create fedora APIM:" + e.getMessage());
-            }
-            
-            //get the parameters from the request
-            String pId=req.getParameter("pid");
-            String dsId=req.getParameter("dsid");
-            String fileUri=req.getParameter("fileUri");
-
-            boolean useNewName=false;
-            if( "true".equals(req.getParameter("useNewName"))){
-                useNewName = true;
-            }
-            if( pId == null || pId.length() == 0 ) 
-                throw new FdcException("Your form submission did not contain " +
-                		"enough information to complete your request.(Missing pid parameter)");
-            if( dsId == null || dsId.length() == 0 ) 
-                throw new FdcException("Your form submission did not contain " +
-                        "enough information to complete your request.(Missing dsid parameter)");
-            if( fileUri == null || fileUri.length() == 0 ) 
-                throw new FdcException("Your form submission did not contain " +
-                        "enough information to complete your request.(Missing fileUri parameter)");
-            
-            FileItem fileRes = req.getFileItem("fileRes"); 
-            if( fileRes == null ) 
-                throw new FdcException("Your form submission did not contain " +
-                "enough information to complete your request.(Missing fileRes)");
-            
-            //check if file individual has a fedora:PID for a data stream
-            VitroRequest vreq = new VitroRequest(rawRequest);
-            IndividualDao iwDao = vreq.getWebappDaoFactory().getIndividualDao();
-            Individual fileEntity = iwDao.getIndividualByURI(fileUri);
-            
-            //check if logged in
-            //TODO: check if logged in
-                               
-            //check if user is allowed to edit datastream
-            //TODO:check if can edit datastream
-            
-            //check if digital object and data stream exist in fedora
-            Datastream ds = apim.getDatastream(pId,dsId,null);
-            if( ds == null )
-                throw new FdcException("There was no datastream in the " +
-                        "repository for " + pId + " " + DEFAULT_DSID);
-                        
-            //upload to temp holding area
-            String originalName = fileRes.getName();
-            String name = originalName.replaceAll("[,+\\\\/$%^&*#@!<>'\"~;]", "_");
-            name = name.replace("..", "_");
-            name = name.trim().toLowerCase();
-
-            String saveLocation = baseDirectoryForFiles + File.separator + name;
-            String savedName = name;
-            int next = 0;
-            boolean foundUnusedName = false;
-            while (!foundUnusedName) {
-                File test = new File(saveLocation);
-                if (test.exists()) {
-                    next++;
-                    savedName = name + '(' + next + ')';
-                    saveLocation = baseDirectoryForFiles + File.separator + savedName;
-                } else {
-                    foundUnusedName = true;
-                }
-            }
-
-            File uploadedFile = new File(saveLocation);
-            
-            try {
-                fileRes.write(uploadedFile);
-            } catch (Exception ex) {
-                log.error("Unable to save POSTed file. " + ex.getMessage());
-                throw new FdcException("Unable to save file to the disk. "
-                        + ex.getMessage());
-            }
-            
-            //upload to temp area on fedora
-            File file = new File(saveLocation);
-            String uploadFileUri = fedora.uploadFile( file );                               
-           // System.out.println("Fedora upload temp = upload file uri is " + uploadFileUri);
-            String md5 = md5hashForFile( file );
-            md5 = md5.toLowerCase();
-            
-            //make change to data stream on fedora
-            apim.modifyDatastreamByReference(pId, dsId, 
-                    null, null, 
-                    fileRes.getContentType(), null, 
-                    uploadFileUri, 
-                    "MD5", null, 
-                    null, false);
-            
-            String checksum =
-                apim.compareDatastreamChecksum(pId,dsId,null);
-
-            //update properties like checksum, file size, and content type
-            
-            WebappDaoFactory wdf = vreq.getWebappDaoFactory();
-            DataPropertyStatement dps = null;
-            DataProperty contentType = wdf.getDataPropertyDao().getDataPropertyByURI(this.contentTypeProperty);
-            if(contentType != null)
-            {
-            	wdf.getDataPropertyStatementDao().deleteDataPropertyStatementsForIndividualByDataProperty(fileEntity, contentType);            
-	            dps = new DataPropertyStatementImpl();
-	            dps.setIndividualURI(fileEntity.getURI());
-	            dps.setDatapropURI(contentType.getURI());
-	            dps.setData(fileRes.getContentType());
-	            wdf.getDataPropertyStatementDao().insertNewDataPropertyStatement(dps);
-            }
-
-            DataProperty fileSize = wdf.getDataPropertyDao().getDataPropertyByURI(this.fileSizeProperty);
-            if(fileSize != null)
-            {
-	            wdf.getDataPropertyStatementDao().deleteDataPropertyStatementsForIndividualByDataProperty(fileEntity, fileSize);            
-	            dps = new DataPropertyStatementImpl();
-	            dps.setIndividualURI(fileEntity.getURI());
-	            dps.setDatapropURI(fileSize.getURI());
-	            dps.setData(Long.toString(fileRes.getSize()));
-	            wdf.getDataPropertyStatementDao().insertNewDataPropertyStatement(dps);
-	            //System.out.println("Updated file size with " + fileRes.getSize());
-            }
-            
-            DataProperty checksumDp = wdf.getDataPropertyDao().getDataPropertyByURI(this.checksumDataProperty);
-            if(checksumDp != null)
-            {
-            	//System.out.println("Checksum data property is also not null");
-	            wdf.getDataPropertyStatementDao().deleteDataPropertyStatementsForIndividualByDataProperty(fileEntity, checksumDp);            
-	            dps = new DataPropertyStatementImpl();
-	            dps.setIndividualURI(fileEntity.getURI());
-	            dps.setDatapropURI(checksumDp.getURI());
-	            dps.setData(checksum);
-	            wdf.getDataPropertyStatementDao().insertNewDataPropertyStatement(dps);
-            }
-       
-            //I'm leaving if statement out for now as the above properties are obviously being replaced as well
-            //if( "true".equals(useNewName)){
-            	//Do we need to encapuslate in this if OR is this path always for replacing a file
-            	//TODO: Put in check to see if file name has changed and only execute these statements if file name has changed
-	            DataProperty fileNameProperty = wdf.getDataPropertyDao().getDataPropertyByURI(this.fileNameProperty);
-	            if(fileNameProperty != null) {
-	            	wdf.getDataPropertyStatementDao().deleteDataPropertyStatementsForIndividualByDataProperty(fileEntity, fileNameProperty);            
-	            	dps = new DataPropertyStatementImpl();
-		            dps.setIndividualURI(fileEntity.getURI());
-		            dps.setDatapropURI(fileNameProperty.getURI());
-		            dps.setData(originalName); //This follows the pattern of the original file upload - the name returned from the uploaded file object
-		            wdf.getDataPropertyStatementDao().insertNewDataPropertyStatement(dps);
-	            	//System.out.println("File name property is not null = " + fileNameProperty.getURI() + " updating to " + originalName);
-	            } else {
-	            	//System.out.println("file name property is null");
-	            }
-	            	            
-	            //Need to also update the check sum node - how would we do that
-	            //Find checksum node related to this particular file uri, then go ahead and update two specific fields
-	            
-	            List<ObjectPropertyStatement >csNodeStatements = fileEntity.getObjectPropertyMap().get(this.checksumNodeProperty).getObjectPropertyStatements();
-	            if(csNodeStatements.size() == 0) {
-	            	System.out.println("No object property statements correspond to this property");
-	            } else {
-	            	ObjectPropertyStatement cnodeStatement = csNodeStatements.get(0);
-	            	String cnodeUri = cnodeStatement.getObjectURI();
-	            	//System.out.println("Checksum node uri is " + cnodeUri);
-	            	
-	            	Individual checksumNodeObject = iwDao.getIndividualByURI(cnodeUri);
-	            	
-	            	DataProperty checksumDateTime = wdf.getDataPropertyDao().getDataPropertyByURI(this.checksumNodeDateTimeProperty);
-	            	if(checksumDateTime != null) {
-	            		 String newDatetime = sessionOntModel.createTypedLiteral(new DateTime()).getString();
-	            		//Review how to update date time
-	            		wdf.getDataPropertyStatementDao().deleteDataPropertyStatementsForIndividualByDataProperty(checksumNodeObject, checksumDateTime);            
-		            	dps = new DataPropertyStatementImpl();
-			            dps.setIndividualURI(checksumNodeObject.getURI());
-			            dps.setDatapropURI(checksumDateTime.getURI());
-			            dps.setData(newDatetime); 
-			            wdf.getDataPropertyStatementDao().insertNewDataPropertyStatement(dps);
-	            		
-	            	}
-	            	DataProperty checksumNodeValue = wdf.getDataPropertyDao().getDataPropertyByURI(this.checksumDataProperty);
-	            	if(checksumNodeValue != null) {
-	            		wdf.getDataPropertyStatementDao().deleteDataPropertyStatementsForIndividualByDataProperty(checksumNodeObject, checksumNodeValue);            
-		            	dps = new DataPropertyStatementImpl();
-			            dps.setIndividualURI(checksumNodeObject.getURI());
-			            dps.setDatapropURI(checksumNodeValue.getURI());
-			            dps.setData(checksum); //Same as fileName above - change if needed
-			            wdf.getDataPropertyStatementDao().insertNewDataPropertyStatement(dps);
-	            	}
-	            	
-	            }
-	            
-	            //Assumes original entity name is equal to the location - as occurs with regular file upload
-	            String originalEntityName = fileEntity.getName();
-	            if(originalEntityName != originalName) {
-	            	//System.out.println("Setting file entity to name of uploaded file");
-	            	fileEntity.setName(originalName);
-	            } else {
-	            	//System.out.println("Conditional for file entity name and uploaded name is saying same");
-	            }
-	           iwDao.updateIndividual(fileEntity);
-            //}
-            
-            req.setAttribute("fileUri", fileUri);
-            req.setAttribute("originalFileName", fileEntity.getName());
-            req.setAttribute("checksum", checksum);
-            if( "true".equals(useNewName)){
-                req.setAttribute("useNewName", "true");
-                req.setAttribute("newFileName", originalName);
-            }else{
-                req.setAttribute("newFileName", fileEntity.getName());
-            }
-            
-            //forward to form     
-            JSPPageHandler.renderBasicPage(req, res, "/fileupload/datastreamModificationSuccess.jsp");
-        }catch(FdcException ex){
-            rawRequest.setAttribute("errors", ex.getMessage());
-            JSPPageHandler.renderPlainPage(rawRequest, res, "/edit/fileUploadError.jsp");
-            return;
-        }
-    }
-    
-    //Delete method
-    public boolean deleteFile(HttpServletRequest req, Individual entity, IndividualDao iwDao, OntModel sessionOntModel) {
-    	boolean success = false;
-    	String fileUri = entity.getURI();
-    	//Create uri based on milliseconds etc.?
-    	Calendar c = Calendar.getInstance();
-    	long timeMs = c.getTimeInMillis();
-    	//Cuirrent date
-	    SimpleDateFormat dateTime = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS");
-		String formattedDeleteDate = dateTime.format(c.getTime());
-    	String deleteEventName = "deleteEvent" + timeMs;
-    	//System.out.println("Delete event name is " +deleteEventName + " - delete time is " + formattedDeleteDate);
-    	
-    	//Get current user
-    	String userURI = LoginStatusBean.getBean(req).getUserURI();
-        //System.out.println("Current logged in user uri is " + userURI); 
-       
-        //Update model
-    	sessionOntModel.enterCriticalSection(true);
-    	
-    	try {
-    		
-    		//Dataset Uri
-    		String datasetUri = (String) req.getAttribute("dataseturi");
-    		//System.out.println("Dataset uri is " + datasetUri);
-    		//Remove the actual relationships: dsr:hasFile and fedora:fromDataSet
-    		ObjectProperty hasFileProperty = sessionOntModel.getObjectProperty(fedoraNs + "hasFile");
-    		
-    		ObjectProperty fromDatasetProperty = sessionOntModel.getObjectProperty(fedoraNs + "fromDataSet");
-    		if(hasFileProperty != null) {
-    			//System.out.println("Has file property does exist");
-    			sessionOntModel.remove(sessionOntModel.createStatement(sessionOntModel.getResource(datasetUri), hasFileProperty, sessionOntModel.getResource(fileUri)));
-    		} else{
-    			//System.out.println("Has file property does not exist");
-    		}
-    		
-    		if(fromDatasetProperty != null) {
-    			//System.out.println("From dataset property exists ");
-    			sessionOntModel.remove(sessionOntModel.createStatement(sessionOntModel.getResource(fileUri), fromDatasetProperty, sessionOntModel.getResource(datasetUri)));
-    		} else{
-    			//System.out.println("From dataset property does not exist");
-    		}
-    		
-    		 
-    		//Create delete event entity and update with the correct information
-    		//Type of Event
-    		Resource deleteEventType = sessionOntModel.createResource(deleteNs + "DeleteEvent");
-    		//Individual event
-	    	Resource eventIndividual = sessionOntModel.createResource(individualPrefix + deleteEventName);
-	    	//Event is of type DeleteEvent
-	    	Statement rType = sessionOntModel.createStatement(eventIndividual, org.apache.jena.vocabulary.RDF.type, deleteEventType);
-	    	sessionOntModel.add(rType);
-	    	//Add properties to individual - deleteDateTime, deletedBy, forDataSet, forFile
-	    	DatatypeProperty dateTimeProp = sessionOntModel.createDatatypeProperty(deleteNs + "deleteDateTime");
-	    	dateTimeProp.setRange(XSD.dateTime);
-	    	
-	    	ObjectProperty deletedByProp = sessionOntModel.createObjectProperty(deleteNs + "deletedBy");
-	    	ObjectProperty forDatasetProp = sessionOntModel.createObjectProperty(deleteNs + "forDataset");
-	    	ObjectProperty forFileProp = sessionOntModel.createObjectProperty(deleteNs + "forFile");
-	    	//Need to make sure date time property is set to correct xsd:DateTime
-	    	//XSDDateTime now = new XSDDateTime(c);
-	    	//XSDDateTime now = new XSDDateTime(java.util.Calendar.getInstance());
-	    	eventIndividual.addProperty(dateTimeProp, sessionOntModel.createTypedLiteral(formattedDeleteDate, XSDDatatype.XSDdateTime));
-	    	//eventIndividual.addProperty(dateTimeProp, sessionOntModel.createTypedLiteral(now, XSDDatatype.XSDdateTime));
-	    	eventIndividual.addProperty(deletedByProp, sessionOntModel.getResource(userURI));
-	    	if(datasetUri != null){
-	    		//System.out.println("Dataset uri is " + datasetUri);
-	    		eventIndividual.addProperty(forDatasetProp, sessionOntModel.getResource(datasetUri));
-	    	}
-	    	eventIndividual.addProperty(forFileProp, sessionOntModel.getResource(fileUri));
-	    	success = true;
-	    	
-    	} finally {
-    		sessionOntModel.leaveCriticalSection();
-    	}
-    	return success;
-    }
-    
-	@Override
-	public void init() throws ServletException {
-		super.init();
-
-		ConfigurationProperties configProperties = ConfigurationProperties
-				.getBean(getServletContext());
-		baseDirectoryForFiles = configProperties.getProperty(
-				"n3.baseDirectoryForFiles", DEFAULT_BASE_DIR);
-
-		String maxSize = configProperties.getProperty("n3.maxSize", Long
-				.toString(DEFAULT_MAX_SIZE));
-		try {
-			maxFileSize = Integer.parseInt(maxSize);
-		} catch (NumberFormatException nfe) {
-			log.error(nfe);
-			maxFileSize = DEFAULT_MAX_SIZE;
-		}
-	}
-   
-    public void setup(OntModel model, ServletContext context) {
-        this.configurationStatus = "";
-        StringBuffer status = new StringBuffer("");
-        
-        if( connected && configured )
-            return;
-        
-        Properties props = new Properties();
-        String path = context.getRealPath(FEDORA_PROPERTIES);
-        try{            
-            InputStream in = new FileInputStream(new File( path ));
-            props.load( in );
-            fedoraUrl = props.getProperty("fedoraUrl");
-            adminUser = props.getProperty("adminUser");
-            adminPassword = props.getProperty("adminPassword");
-            pidNamespace = props.getProperty("pidNamespace");
-            
-            if( fedoraUrl == null || adminUser == null || adminPassword == null ){
-                if( fedoraUrl == null ){
-                    log.error("'fedoraUrl' not found in properties file");        
-                    status.append("<p>'fedoraUrl' not found in properties file.</p>\n");
-                }
-                if( adminUser == null ) {
-                    log.error("'adminUser' was not found in properties file, the " +
-                          "user name of the fedora admin is needed to access the " +
-                            "fedora API-M services.");                    
-                    status.append("<p>'adminUser' was not found in properties file, the " +
-                            "user name of the fedora admin is needed to access the " +
-                              "fedora API-M services.</p>\n");
-                }
-                if( adminPassword == null ){
-                    log.error("'adminPassword' was not found in properties file, the " +
-                    "admin password is needed to access the fedora API-M services.");
-                    status.append("<p>'adminPassword' was not found in properties file, the " +
-                    "admin password is needed to access the fedora API-M services.</p>\n");
-                }
-                if( pidNamespace == null ){
-                    log.error("'pidNamespace' was not found in properties file, the " +
-                    "PID namespace indicates which namespace to use when creating " +
-                    "new fedor digital objects.");
-                    status.append("<p>'pidNamespace' was not found in properties file, the " +
-                            "PID namespace indicates which namespace to use when creating " +
-                            "new fedor digital objects.</p>\n");
-                } 
-                fedoraUrl = null; adminUser = null; adminPassword = null;
-                configured = false;
-            }  else {
-                configured = true;
-            }
-        }catch(FileNotFoundException e) {
-            log.error("No fedora.properties file found,"+ 
-                    "it should be located at " + path);
-            status.append("<h1>Fedora configuration failed.</h1>\n");
-            status.append("<p>No fedora.properties file found,"+ 
-                    "it should be located at " + path + "</p>\n");
-            configured = false;
-            return;
-        }catch(Exception ex){            
-            status.append("<p>Fedora configuration failed.</p>\n");
-            status.append("<p>Exception while loading" + path + "</p>\n");
-            status.append("<p>" + ex.getMessage() + "</p>\n"); 
-            log.error("could not load fedora properties", ex);
-            fedoraUrl = null; adminUser = null; adminPassword = null;
-            configured = false;
-            return;
-        }
-         
-        
-        status.append(RELOAD_MSG); 
-        this.configurationStatus += status.toString();
-//       else{
-//            status.append("<h2>Fedora configuration file ").append(path).append(" was loaded</h2>");
-//            status.append("<p>fedoraUrl: ").append(fedoraUrl).append("</p>\n");
-//            checkFedoraServer();
-//        }
-    }
-    
-    private boolean canConnectToFedoraServer( ){
-        try{
-            FedoraClient fc = new FedoraClient(fedoraUrl,adminUser, adminPassword);
-            String fedoraVersion = fc.getServerVersion();
-            if( fedoraVersion != null && fedoraVersion.length() > 0 ){
-                configurationStatus += "<p>Fedora server is live and is running " +
-                        "fedora version " + fedoraVersion + "</p>\n";
-                connected = true;
-                return true;
-            } else {
-                configurationStatus += "<p>Unable to reach fedora server</p>\n";
-                connected = false;
-                return false;
-            }
-        }catch (Exception e) {
-            configurationStatus += "<p>There was an error while checking the " +
-                    "fedora server version</p>\n<p>"+ e.getMessage() + "</p>\n";
-            connected = false;
-            return false;            
-        }                            
-    }
-    
-    public boolean isConfigured(){ return configured; }
-    public boolean isConnected(){ return connected; }
-    
-    private class FdcException extends Exception {
-        public FdcException(String message) {
-            super(message);           
-        }
-    }
-    
-    private static final String RELOAD_MSG = 
-        "<p>The fedora configuartion file will be reloaded if " +
-        "you edit the properties file and check the status.</p>\n";
-
-    public static String md5hashForFile(File file){  
-        try {
-            InputStream fin = new FileInputStream(file);
-            java.security.MessageDigest md5er =
-                MessageDigest.getInstance("MD5");
-            byte[] buffer = new byte[1024];
-            int read;
-            do {
-                read = fin.read(buffer);
-                if (read > 0)
-                    md5er.update(buffer, 0, read);
-            } while (read != -1);
-            fin.close();
-            byte[] digest = md5er.digest();
-            if (digest == null)
-                return null;
-            String strDigest = "0x";
-            for (int i = 0; i < digest.length; i++) {
-                strDigest += Integer.toString((digest[i] & 0xff) 
-                        + 0x100, 16).substring(1);
-            }
-            return strDigest;
-        } catch (Exception e) {
-            return null;
-        }        
-    }
-    
-    private static final Log log = LogFactory.getLog(FedoraDatastreamController.class.getName());
-}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/UserAccountsSelector.java

@@ -20,9 +20,9 @@ import org.apache.jena.rdf.model.Resource;
 import edu.cornell.mannlib.vitro.webapp.beans.UserAccount;
 import edu.cornell.mannlib.vitro.webapp.beans.UserAccount.Status;
 import edu.cornell.mannlib.vitro.webapp.controller.accounts.UserAccountsOrdering.Field;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner.QueryParser;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.sparql.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.ResultSetParser;
+import edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.SparqlQueryRunner;
 
 /**
  * Pull some UserAccounts from the model, based on a set of criteria.
@@ -111,8 +111,9 @@ public class UserAccountsSelector {
 				.replace("%offset%", offset());
 		log.debug("main query: " + qString);
 
-		List<UserAccount> accounts = new SparqlQueryRunner(model)
-				.executeSelect(new MainQueryParser(), qString);
+		List<UserAccount> accounts = SparqlQueryRunner
+				.createSelectQueryContext(model, qString).execute()
+				.parse(new MainQueryParser());
 		log.debug("query returns: " + accounts);
 		return accounts;
 	}
@@ -126,8 +127,8 @@ public class UserAccountsSelector {
 				.replace("%filterClauses%", filterClauses());
 		log.debug("count query: " + qString);
 
-		int count = new SparqlQueryRunner(model).executeSelect(
-				new CountQueryParser(), qString);
+		int count = SparqlQueryRunner.createSelectQueryContext(model, qString)
+				.execute().parse(new CountQueryParser());
 		log.debug("result count: " + count);
 		return count;
 	}
@@ -139,8 +140,9 @@ public class UserAccountsSelector {
 					PREFIX_LINES).replace("%uri%", uri);
 			log.debug("permissions query: " + qString);
 
-			Set<String> permissions = new SparqlQueryRunner(model)
-					.executeSelect(new PermissionsQueryParser(), qString);
+			Set<String> permissions = SparqlQueryRunner
+					.createSelectQueryContext(model, qString).execute()
+					.parse(new PermissionsQueryParser());
 			log.debug("permissions for '" + uri + "': " + permissions);
 			account.setPermissionSetUris(permissions);
 		}
@@ -214,7 +216,8 @@ public class UserAccountsSelector {
 		return String.valueOf(offset);
 	}
 
-	private static class MainQueryParser extends QueryParser<List<UserAccount>> {
+	private static class MainQueryParser extends
+			ResultSetParser<List<UserAccount>> {
 		@Override
 		protected List<UserAccount> defaultValue() {
 			return Collections.emptyList();
@@ -274,7 +277,7 @@ public class UserAccountsSelector {
 		}
 	}
 
-	private static class CountQueryParser extends QueryParser<Integer> {
+	private static class CountQueryParser extends ResultSetParser<Integer> {
 		@Override
 		protected Integer defaultValue() {
 			return 0;
@@ -299,7 +302,7 @@ public class UserAccountsSelector {
 	}
 
 	private static class PermissionsQueryParser extends
-			QueryParser<Set<String>> {
+			ResultSetParser<Set<String>> {
 		@Override
 		protected Set<String> defaultValue() {
 			return Collections.emptySet();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ProxyRelationshipSelector.java

@@ -16,9 +16,9 @@ import org.apache.jena.query.ResultSet;
 import edu.cornell.mannlib.vitro.webapp.controller.accounts.manageproxies.ProxyRelationshipSelectionBuilder.ItemInfo;
 import edu.cornell.mannlib.vitro.webapp.controller.accounts.manageproxies.ProxyRelationshipSelectionBuilder.Relationship;
 import edu.cornell.mannlib.vitro.webapp.controller.accounts.manageproxies.ProxyRelationshipSelectionCriteria.ProxyRelationshipView;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner.QueryParser;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.sparql.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.ResultSetParser;
+import edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.SparqlQueryRunner;
 
 /**
  * A class which will accept a ProxyRelationshipSelectionCriteria and produce a
@@ -94,8 +94,9 @@ public class ProxyRelationshipSelector {
 				PREFIX_LINES);
 		qString = replaceFilterClauses(qString);
 
-		int count = new SparqlQueryRunner(context.userAccountsModel)
-				.executeSelect(new CountQueryParser(), qString);
+		int count = SparqlQueryRunner
+				.createSelectQueryContext(context.userAccountsModel, qString)
+				.execute().parse(new CountQueryParser());
 
 		log.debug("result count: " + count);
 		builder.count = count;
@@ -136,9 +137,9 @@ public class ProxyRelationshipSelector {
 				.replace("%offset%", offset());
 		qString = replaceFilterClauses(qString);
 
-		List<Relationship> relationships = new SparqlQueryRunner(
-				context.userAccountsModel).executeSelect(
-				new ProxyBasicsParser(), qString);
+		List<Relationship> relationships = SparqlQueryRunner
+				.createSelectQueryContext(context.userAccountsModel, qString)
+				.execute().parse(new ProxyBasicsParser());
 		log.debug("getProxyBasics returns: " + relationships);
 		builder.relationships.addAll(relationships);
 	}
@@ -177,8 +178,9 @@ public class ProxyRelationshipSelector {
 						.replace("%matchingProperty%", context.matchingProperty)
 						.replace("%externalAuthId%", proxy.externalAuthId);
 
-				ItemInfo expansion = new SparqlQueryRunner(context.unionModel)
-						.executeSelect(new ExpandProxyParser(), qString);
+				ItemInfo expansion = SparqlQueryRunner
+						.createSelectQueryContext(context.unionModel, qString)
+						.execute().parse(new ExpandProxyParser());
 				proxy.classLabel = expansion.classLabel;
 				proxy.imageUrl = expansion.imageUrl;
 			}
@@ -199,9 +201,10 @@ public class ProxyRelationshipSelector {
 				String qString = QUERY_RELATIONSHIPS.replace("%prefixes%",
 						PREFIX_LINES).replace("%proxyUri%", proxy.uri);
 
-				List<String> profileUris = new SparqlQueryRunner(
-						context.userAccountsModel).executeSelect(
-						new RelationshipsParser(), qString);
+				List<String> profileUris = SparqlQueryRunner
+						.createSelectQueryContext(context.userAccountsModel,
+								qString).execute()
+						.parse(new RelationshipsParser());
 
 				for (String profileUri : profileUris) {
 					r.profileInfos
@@ -235,8 +238,9 @@ public class ProxyRelationshipSelector {
 				String qString = QUERY_EXPAND_PROFILE.replace("%prefixes%",
 						PREFIX_LINES).replace("%profileUri%", profile.uri);
 
-				ItemInfo expansion = new SparqlQueryRunner(context.unionModel)
-						.executeSelect(new ExpandProfileParser(), qString);
+				ItemInfo expansion = SparqlQueryRunner
+						.createSelectQueryContext(context.unionModel, qString)
+						.execute().parse(new ExpandProfileParser());
 				profile.label = expansion.label;
 				profile.classLabel = expansion.classLabel;
 				profile.imageUrl = expansion.imageUrl;
@@ -285,7 +289,7 @@ public class ProxyRelationshipSelector {
 	// ----------------------------------------------------------------------
 
 	private static class ProxyBasicsParser extends
-			QueryParser<List<Relationship>> {
+			ResultSetParser<List<Relationship>> {
 		@Override
 		protected List<Relationship> defaultValue() {
 			return Collections.emptyList();
@@ -318,7 +322,7 @@ public class ProxyRelationshipSelector {
 		}
 	}
 
-	private static class CountQueryParser extends QueryParser<Integer> {
+	private static class CountQueryParser extends ResultSetParser<Integer> {
 		@Override
 		protected Integer defaultValue() {
 			return 0;
@@ -342,7 +346,7 @@ public class ProxyRelationshipSelector {
 		}
 	}
 
-	private static class ExpandProxyParser extends QueryParser<ItemInfo> {
+	private static class ExpandProxyParser extends ResultSetParser<ItemInfo> {
 		@Override
 		protected ItemInfo defaultValue() {
 			return new ItemInfo();
@@ -367,7 +371,8 @@ public class ProxyRelationshipSelector {
 		}
 	}
 
-	private static class RelationshipsParser extends QueryParser<List<String>> {
+	private static class RelationshipsParser extends
+			ResultSetParser<List<String>> {
 		@Override
 		protected List<String> defaultValue() {
 			return Collections.emptyList();
@@ -388,7 +393,7 @@ public class ProxyRelationshipSelector {
 		}
 	}
 
-	private static class ExpandProfileParser extends QueryParser<ItemInfo> {
+	private static class ExpandProfileParser extends ResultSetParser<ItemInfo> {
 		@Override
 		protected ItemInfo defaultValue() {
 			return new ItemInfo();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ajax/BasicProxiesGetter.java

@@ -24,8 +24,8 @@ import edu.cornell.mannlib.vitro.webapp.controller.ajax.AbstractAjaxResponder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.sparql.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.SparqlQueryRunner;
 import edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil;
 
 /**
@@ -76,10 +76,10 @@ public class BasicProxiesGetter extends AbstractAjaxResponder {
 			String cleanTerm = SparqlQueryUtils.escapeForRegex(term);
 			String queryStr = QUERY_BASIC_PROXIES.replace("%term%", cleanTerm);
 
-			JSONArray jsonArray = new SparqlQueryRunner(userAccountsModel)
-					.executeSelect(
-							new BasicProxyInfoParser(placeholderImageUrl),
-							queryStr);
+			JSONArray jsonArray = SparqlQueryRunner
+					.createSelectQueryContext(userAccountsModel, queryStr)
+					.execute()
+					.parse(new BasicProxyInfoParser(placeholderImageUrl));
 
 			String response = jsonArray.toString();
 			log.debug(response);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/accounts/user/UserAccountsFirstTimeExternalPage.java

@@ -9,7 +9,7 @@ import java.util.Map;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpSession;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.PermissionSets;
 import edu.cornell.mannlib.vitro.webapp.beans.UserAccount;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/RestrictLoginsController.java

@@ -16,6 +16,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServ
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
+import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 
 /**
  * Offer the user the ability to apply a RestrictedAuthenticator or revert to a
@@ -80,7 +81,7 @@ public class RestrictLoginsController extends FreemarkerHttpServlet {
 			boolean restricted = figureCurrentlyState() == State.RESTRICTED;
 
 			Map<String, Object> body = new HashMap<String, Object>();
-			body.put("title", "Restrict Logins");
+			body.put("title", I18n.text(vreq, "restrict_logins"));
 			body.put("restricted", restricted);
 			if (!MESSAGE_NO_MESSAGE.equals(messageCode)) {
 				body.put(messageCode, Boolean.TRUE);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/SparqlQueryController.java

@@ -16,7 +16,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -36,9 +36,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.http.AcceptHeaderParsingException;
 import edu.cornell.mannlib.vitro.webapp.utils.http.NotAcceptableException;
+import edu.cornell.mannlib.vitro.webapp.utils.sparql.SparqlQueryUtils;
 
 /**
  * Present the SPARQL Query form, and execute the queries.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/StartupStatusController.java

@@ -11,6 +11,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
+import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 /**
@@ -27,7 +28,7 @@ public class StartupStatusController extends FreemarkerHttpServlet {
 	protected ResponseValues processRequest(VitroRequest vreq) {
 		Map<String, Object> body = new HashMap<String, Object>();
 
-		body.put("title", "Startup Status");
+		body.put("title", I18n.text(vreq, "startup_status"));
 		body.put("status", StartupStatus.getBean(getServletContext()));
 		body.put("contextPath", getContextPath());
 		body.put("applicationName", getApplicationName(vreq));

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/AbstractAjaxResponder.java

@@ -24,7 +24,7 @@ import org.apache.jena.query.ResultSet;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.UserAccountsDao;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner;
+import edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.ResultSetParser;
 
 /**
  * A base class for AJAX responder objects, to be instantiated and invoked by
@@ -82,7 +82,7 @@ public abstract class AbstractAjaxResponder {
 	 */
 	protected String assembleJsonResponse(List<Map<String, String>> maps) {
 		JSONArray jsonArray = new JSONArray();
-		for (Map<String, String> map: maps) {
+		for (Map<String, String> map : maps) {
 			jsonArray.put(map);
 		}
 		return jsonArray.toString();
@@ -93,7 +93,7 @@ public abstract class AbstractAjaxResponder {
 	 * implement "parseSolutionRow()"
 	 */
 	protected abstract static class JsonArrayParser extends
-			SparqlQueryRunner.QueryParser<JSONArray> {
+			ResultSetParser<JSONArray> {
 		@Override
 		protected JSONArray defaultValue() {
 			return new JSONArray();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/api/SparqlUpdateApiController.java

@@ -14,7 +14,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/api/sparqlquery/SparqlQueryApiExecutor.java

@@ -10,9 +10,9 @@ import org.apache.jena.query.QueryParseException;
 
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.http.AcceptHeaderParsingException;
 import edu.cornell.mannlib.vitro.webapp.utils.http.NotAcceptableException;
+import edu.cornell.mannlib.vitro.webapp.utils.sparql.SparqlQueryUtils;
 
 /**
  * The base class for the SPARQL query API.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/authenticate/LoginRedirector.java

@@ -11,7 +11,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.servlet.http.HttpSession;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/datatools/dumprestore/DumpRestoreController.java

@@ -11,7 +11,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/PrimitiveDelete.java

@@ -6,7 +6,7 @@ import static javax.servlet.http.HttpServletResponse.SC_UNAUTHORIZED;
 
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/ReorderController.java

@@ -32,6 +32,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 
+import java.io.IOException;
+
 /**
  * This controller receives Ajax requests for reordering a list of individuals. 
  * Parameters:
@@ -103,9 +105,12 @@ public class ReorderController extends VitroAjaxController {
         // we only hit the database once?
         reorderIndividuals(individualUris, vreq, rankPredicate);
 
-        
        response.setStatus(SC_OK);
-        
+       try {
+           response.getWriter().write("{}");
+       } catch (IOException e) {
+           e.printStackTrace();
+       }
     }
     
     private void reorderIndividuals(String[] individualUris, VitroRequest vreq, String rankPredicate) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/AllClassGroupsListingController.java

@@ -11,7 +11,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import edu.cornell.mannlib.vitro.webapp.utils.JSPPageHandler;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import edu.cornell.mannlib.vedit.controller.BaseEditController;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/PropertyGroupsListingController.java

@@ -14,7 +14,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import edu.cornell.mannlib.vitro.webapp.utils.JSPPageHandler;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ContactFormController.java

@@ -5,7 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/DumpTestController.java

@@ -13,7 +13,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import org.apache.commons.lang.time.DateUtils;
+import org.apache.commons.lang3.time.DateUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/FreemarkerComponentGenerator.java

@@ -7,7 +7,7 @@ import java.util.Map;
 import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/FreemarkerHttpServlet.java

@@ -17,7 +17,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/IndividualListController.java

@@ -9,7 +9,7 @@ import java.util.List;
 import java.util.Map;
 
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist.ListedIndividualBuilder;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -22,6 +22,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Res
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.individuallist.IndividualListResults;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
+import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngineException;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchQuery;
 import edu.cornell.mannlib.vitro.webapp.utils.searchengine.SearchQueryUtils;
@@ -94,7 +95,7 @@ public class IndividualListController extends FreemarkerHttpServlet {
                         vclass.getURI(), 
                         page, 
                         alpha, 
-                        vreq.getWebappDaoFactory().getIndividualDao());                                
+                        vreq);                                
                 body.putAll(vcResults.asFreemarkerMap());
 
                 List<Individual> inds = vcResults.getEntities();
@@ -148,12 +149,12 @@ public class IndividualListController extends FreemarkerHttpServlet {
         return SearchQueryUtils.getPageParameter(request);
     }
     
-    public static IndividualListResults getResultsForVClass(String vclassURI, int page, String alpha, IndividualDao indDao) 
+    public static IndividualListResults getResultsForVClass(String vclassURI, int page, String alpha, VitroRequest vreq) 
     throws SearchException{
    	 	try{
             List<String> classUris = Collections.singletonList(vclassURI);
-			IndividualListQueryResults results = buildAndExecuteVClassQuery(classUris, alpha, page, INDIVIDUALS_PER_PAGE, indDao);
-	        return getResultsForVClassQuery(results, page, INDIVIDUALS_PER_PAGE, alpha);
+			IndividualListQueryResults results = buildAndExecuteVClassQuery(classUris, alpha, page, INDIVIDUALS_PER_PAGE, vreq.getWebappDaoFactory().getIndividualDao());
+	        return getResultsForVClassQuery(results, page, INDIVIDUALS_PER_PAGE, alpha, vreq);
    	 	} catch (SearchEngineException e) {
    	 	    String msg = "An error occurred retrieving results for vclass query";
    	 	    log.error(msg, e);
@@ -165,31 +166,31 @@ public class IndividualListController extends FreemarkerHttpServlet {
 	    }
     }
     
-    public static IndividualListResults getResultsForVClassIntersections(List<String> vclassURIs, int page, int pageSize, String alpha, IndividualDao indDao) {
+    public static IndividualListResults getResultsForVClassIntersections(List<String> vclassURIs, int page, int pageSize, String alpha, VitroRequest vreq) {
         try{
-            IndividualListQueryResults results = buildAndExecuteVClassQuery(vclassURIs, alpha, page, pageSize, indDao);
-	        return getResultsForVClassQuery(results, page, pageSize, alpha);
+            IndividualListQueryResults results = buildAndExecuteVClassQuery(vclassURIs, alpha, page, pageSize, vreq.getWebappDaoFactory().getIndividualDao());
+	        return getResultsForVClassQuery(results, page, pageSize, alpha, vreq);
         } catch(Throwable th) {
        	    log.error("Error retrieving individuals corresponding to intersection multiple classes." + vclassURIs.toString(), th);
        	    return IndividualListResults.EMPTY;
         }
     }
 	
-    public static IndividualListResults getRandomResultsForVClass(String vclassURI, int page, int pageSize, IndividualDao indDao) {
+    public static IndividualListResults getRandomResultsForVClass(String vclassURI, int page, int pageSize, VitroRequest vreq) {
    	 	try{
             List<String> classUris = Collections.singletonList(vclassURI);
-			IndividualListQueryResults results = buildAndExecuteRandomVClassQuery(classUris, page, pageSize, indDao);
-	        return getResultsForVClassQuery(results, page, pageSize, "");
+			IndividualListQueryResults results = buildAndExecuteRandomVClassQuery(classUris, page, pageSize, vreq.getWebappDaoFactory().getIndividualDao());
+	        return getResultsForVClassQuery(results, page, pageSize, "", vreq);
    	 	} catch(Throwable th) {
 	   		log.error("An error occurred retrieving random results for vclass query", th);
 	   		return IndividualListResults.EMPTY;
 	    }
     }
 
-	private static IndividualListResults getResultsForVClassQuery(IndividualListQueryResults results, int page, int pageSize, String alpha) {
+	private static IndividualListResults getResultsForVClassQuery(IndividualListQueryResults results, int page, int pageSize, String alpha, VitroRequest vreq) {
         long hitCount = results.getHitCount();
         if ( hitCount > pageSize ){
-        	return new IndividualListResults(hitCount, results.getIndividuals(), alpha, true, makePagesList(hitCount, pageSize, page));
+        	return new IndividualListResults(hitCount, results.getIndividuals(), alpha, true, makePagesList(hitCount, pageSize, page, vreq));
         }else{
         	return new IndividualListResults(hitCount, results.getIndividuals(), alpha, false, Collections.<PageRecord>emptyList());
         }
@@ -221,7 +222,7 @@ public class IndividualListController extends FreemarkerHttpServlet {
 	}
 
     
-    public static List<PageRecord> makePagesList( long size, int pageSize,  int selectedPage ) {        
+    public static List<PageRecord> makePagesList( long size, int pageSize,  int selectedPage , VitroRequest vreq) {        
 
         List<PageRecord> records = new ArrayList<PageRecord>( MAX_PAGES + 1 );
         int requiredPages = (int) (size/pageSize) ;
@@ -234,7 +235,7 @@ public class IndividualListController extends FreemarkerHttpServlet {
             for(int page = 1; page < requiredPages && page <= MAX_PAGES ; page++ ){
                 records.add( new PageRecord( "page=" + page, Integer.toString(page), Integer.toString(page), selectedPage == page ) );            
             }
-            records.add( new PageRecord( "page="+ (MAX_PAGES+1), Integer.toString(MAX_PAGES+1), "more...", false));
+            records.add( new PageRecord( "page="+ (MAX_PAGES+1), Integer.toString(MAX_PAGES+1), I18n.text(vreq, "paging_link_more"), false));
         }else if( requiredPages > MAX_PAGES && selectedPage+1 > MAX_PAGES && selectedPage < requiredPages - MAX_PAGES){
             //the selected pages is in the middle of the list of page
             int startPage = selectedPage - MAX_PAGES / 2;
@@ -242,7 +243,7 @@ public class IndividualListController extends FreemarkerHttpServlet {
             for(int page = startPage; page <= endPage ; page++ ){
                 records.add( new PageRecord( "page=" + page, Integer.toString(page), Integer.toString(page), selectedPage == page ) );            
             }
-            records.add( new PageRecord( "page="+ (endPage+1), Integer.toString(endPage+1), "more...", false));
+            records.add( new PageRecord( "page="+ (endPage+1), Integer.toString(endPage+1), I18n.text(vreq, "paging_link_more"), false));
         }else if ( requiredPages > MAX_PAGES && selectedPage > requiredPages - MAX_PAGES ){
             //the selected page is in the end of the list 
             int startPage = requiredPages - MAX_PAGES;      

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListClassGroupsController.java

@@ -9,7 +9,7 @@ import java.util.Map;
 
 import net.sf.json.util.JSONUtils;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyGroupsController.java

@@ -10,7 +10,7 @@ import java.util.Map;
 
 import net.sf.json.util.JSONUtils;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/PageController.java

@@ -14,7 +14,7 @@ import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -27,6 +27,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
+import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.DataGetter;
 import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.DataGetterUtils;
 /**
@@ -188,23 +189,23 @@ public class PageController extends FreemarkerHttpServlet{
 
     private ResponseValues doError(VitroRequest vreq) {
         Map<String, Object> body = new HashMap<String, Object>();
-        body.put("title","Page could not be created");
-        body.put("errorMessage", "There was an error while creating the page, please check the logs.");        
+        body.put("title", I18n.text(vreq, "page_not_created"));
+        body.put("errorMessage", I18n.text(vreq, "page_not_created_msg"));        
         return new TemplateResponseValues(Template.TITLED_ERROR_MESSAGE.toString(), body, HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
     }
 
     private ResponseValues doNotFound(VitroRequest vreq) {
         Map<String, Object> body = new HashMap<String, Object>();
-        body.put("title","Page Not Found");
-        body.put("errorMessage", "The page was not found in the system.");        
+        body.put("title", I18n.text(vreq, "page_not_found"));
+        body.put("errorMessage", I18n.text(vreq, "page_not_found_msg"));        
         return new TemplateResponseValues(Template.TITLED_ERROR_MESSAGE.toString(), body, HttpServletResponse.SC_NOT_FOUND);
     }
 
 
     private ResponseValues doNoPageSpecified(VitroRequest vreq) {
         Map<String, Object> body = new HashMap<String, Object>();
-        body.put("title","No page URI specified");
-        body.put("errorMessage", "Could not generate page beacause it was unclear what page was being requested.  A URL mapping may be missing.");        
+        body.put("title",I18n.text(vreq, "page_uri_missing"));
+        body.put("errorMessage", I18n.text(vreq, "page_uri_missing_msg"));        
         return new TemplateResponseValues(Template.TITLED_ERROR_MESSAGE.toString(), body, HttpServletResponse.SC_NOT_FOUND);
     }
     

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/StaticPageController.java

@@ -5,12 +5,14 @@ package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
+import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 
 /*
  * Servlet that only specifies a template, without putting any data
@@ -33,7 +35,7 @@ public class StaticPageController extends FreemarkerHttpServlet {
         String requestedUrl = vreq.getServletPath();
         String title = null;
         if (requestedUrl.equals("/login")) {
-            title = "Log in to " + siteName;
+            title = StringUtils.capitalize(I18n.text(vreq, "log_in")) + " - " + siteName;
         }
         return title;
     }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/UrlBuilder.java

@@ -71,7 +71,7 @@ public class UrlBuilder {
     
     public enum Css {
         CUSTOM_FORM("/edit/forms/css/customForm.css"),
-        JQUERY_UI("/js/jquery-ui/css/smoothness/jquery-ui-1.8.9.custom.css");        
+        JQUERY_UI("/js/jquery-ui/css/smoothness/jquery-ui-1.12.1.css");
 
         private final String path;
         
@@ -90,8 +90,9 @@ public class UrlBuilder {
     
     public enum JavaScript {
         CUSTOM_FORM_UTILS("/js/customFormUtils.js"),
-        JQUERY("/js/jquery.js"),
-        JQUERY_UI("/js/jquery-ui/js/jquery-ui-1.8.9.custom.min.js"),
+        JQUERY("/js/jquery-1.12.4.min.js"),
+        JQUERY_MIGRATE("/js/jquery-migrate-1.4.1.js"),
+        JQUERY_UI("/js/jquery-ui/js/jquery-ui-1.12.1.min.js"),
         UTILS("/js/utils.js");
         
         private final String path;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/grefine/JSONReconcileServlet.java

@@ -15,7 +15,7 @@ import javax.servlet.ServletOutputStream;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.json.JSONArray;
@@ -470,18 +470,10 @@ public class JSONReconcileServlet extends VitroHttpServlet {
             return label;
         }
         
-        public String getJsonLabel() {
-            return JSONObject.quote(label);
-        }
-        
         public String getUri() {
             return uri;
         }
         
-        public String getJsonUri() {
-            return JSONObject.quote(uri);
-        }
-        
         Map<String, String> toMap() {
             Map<String, String> map = new HashMap<String, String>();
             map.put("label", label);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualController.java

@@ -21,6 +21,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Exc
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.RedirectResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
+import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 
 /**
  * Handles requests for entity information.
@@ -74,7 +75,7 @@ public class IndividualController extends FreemarkerHttpServlet {
 				 * If we can't figure out what individual you want, or if there
 				 * is no such individual, show an informative error page.
 				 */
-				return doNotFound();
+				return doNotFound(vreq);
 			case BYTESTREAM_REDIRECT:
 				/*
 				 * If the Individual requested is a FileBytestream, redirect
@@ -116,10 +117,10 @@ public class IndividualController extends FreemarkerHttpServlet {
 				new IndividualRequestAnalysisContextImpl(vreq)).analyze();
 	}
 
-	private ResponseValues doNotFound() {
+	private ResponseValues doNotFound(VitroRequest vreq) {
 		Map<String, Object> body = new HashMap<String, Object>();
-		body.put("title", "Individual Not Found");
-		body.put("errorMessage", "The individual was not found in the system.");
+		body.put("title", I18n.text(vreq, "individual_not_found"));
+		body.put("errorMessage", I18n.text(vreq, "individual_not_found_msg"));
 
 		return new TemplateResponseValues(TEMPLATE_HELP, body,
 				HttpServletResponse.SC_NOT_FOUND);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRdfAssembler.java

@@ -10,7 +10,7 @@ import java.util.Set;
 
 import javax.servlet.ServletContext;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/individuallist/IndividualListResultsUtils.java

@@ -8,7 +8,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.json.JSONArray;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaCsv2RdfController.java

@@ -141,7 +141,7 @@ public class JenaCsv2RdfController extends JenaIngestController {
     }
 
 	 public Model doExecuteCsv2Rdf(VitroRequest vreq, FileItem fileStream, String filePath) throws Exception {
-			char[] quoteChars = {'"'};
+			char quoteChar = '"';
 			String namespace = "";
 			String tboxNamespace = vreq.getParameter("tboxNamespace");
 			String typeName = vreq.getParameter("typeName");
@@ -162,7 +162,7 @@ public class JenaCsv2RdfController extends JenaIngestController {
 				separatorChar = '\t';
 			}
 			
-			Csv2Rdf c2r = new Csv2Rdf(separatorChar, quoteChars,namespace,tboxNamespace,typeName);
+			Csv2Rdf c2r = new Csv2Rdf(separatorChar, quoteChar,namespace,tboxNamespace,typeName);
 			
 			InputStream is = null;
 			

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

@@ -33,7 +33,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import edu.cornell.mannlib.vitro.webapp.utils.JSPPageHandler;
-import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.semanticweb.owlapi.reasoner.InconsistentOntologyException;
@@ -73,12 +73,12 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.VitroModelFactory;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestWorkflowProcessor;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.WorkflowOntology;
+import edu.cornell.mannlib.vitro.webapp.utils.sparql.SparqlQueryUtils;
 
 public class JenaIngestController extends BaseEditController {
 	private static final Log log = LogFactory.getLog(JenaIngestController.class);
@@ -861,7 +861,7 @@ public class JenaIngestController extends BaseEditController {
                 Individual ind = jenaOntModel.getIndividual(savedQueryURIStr);
                 log.debug("Using query "+savedQueryURIStr);
                 queryStr = ( (Literal) ind.getPropertyValue(queryStrProp)).getLexicalForm();
-                queryStr = StringEscapeUtils.unescapeHtml(queryStr); // !!! We need to turn off automatic HTML-escaping for data property editing.
+                queryStr = StringEscapeUtils.UNESCAPE_HTML4.translate(queryStr); // !!! We need to turn off automatic HTML-escaping for data property editing.
             } finally {
                 jenaOntModel.leaveCriticalSection();
             }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/json/JsonProducer.java

@@ -7,7 +7,7 @@ import java.util.List;
 
 import javax.servlet.ServletException;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.json.JSONArray;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/json/JsonServlet.java

@@ -109,7 +109,7 @@ public class JsonServlet extends VitroHttpServlet {
 	                 vclassURIs, 
 	                 page, INDIVIDUALS_PER_PAGE,
 	                 alpha, 
-	                 vreq.getWebappDaoFactory().getIndividualDao());  
+	                 vreq);  
         } catch(Exception ex) {
         	log.error("Error in retrieval of search results for VClass " + vclassURIs.toString(), ex);
         	return IndividualListResults.EMPTY;
@@ -144,7 +144,7 @@ public class JsonServlet extends VitroHttpServlet {
  	                 vclassURI, 
  	                 page, 
  	                 pageSize, 
- 	                 vreq.getWebappDaoFactory().getIndividualDao());  
+ 	                 vreq);  
          } catch(Exception ex) {
          	log.error("Error in retrieval of search results for VClass " + vclassURI, ex);
          	return IndividualListResults.EMPTY;

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

@@ -33,7 +33,7 @@ public class VitroVocabulary {
     public static final String OWL_ONTOLOGY = OWL+"Ontology";
     public static final String OWL_THING = OWL+"Thing";
     
-    public static final String AFN = "http://jena.hpl.hp.com/ARQ/function#";
+    public static final String AFN = "http://jena.apache.org/ARQ/function#";
 
     public static final String label = vitroURI + "label";
     

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

@@ -13,7 +13,7 @@ import java.util.List;
 import java.util.Map;
 
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/FauxPropertyDaoJena.java

@@ -2,9 +2,9 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
+import static edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.SparqlQueryRunner.createSelectQueryContext;
+import static edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.SparqlQueryRunner.queryHolder;
 import static org.apache.jena.rdf.model.ResourceFactory.createResource;
-import static edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner.bindValues;
-import static edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner.uriValue;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -16,7 +16,6 @@ import java.util.Set;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-
 import org.apache.jena.ontology.ObjectProperty;
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.ontology.OntModelSpec;
@@ -33,11 +32,11 @@ import edu.cornell.mannlib.vitro.webapp.beans.FauxProperty;
 import edu.cornell.mannlib.vitro.webapp.dao.FauxPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner;
-import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner.QueryParser;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.criticalsection.LockableOntModel;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.criticalsection.LockableOntModelSelector;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.criticalsection.LockedOntModel;
+import edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.QueryHolder;
+import edu.cornell.mannlib.vitro.webapp.utils.sparqlrunner.ResultSetParser;
 
 /**
  * TODO
@@ -522,7 +521,7 @@ public class FauxPropertyDaoJena extends JenaBaseDao implements FauxPropertyDao
 			+ "} \n"; //
 
 	private static class ParserLocateConfigContext extends
-			QueryParser<Set<ConfigContext>> {
+			ResultSetParser<Set<ConfigContext>> {
 		private final String domainUri;
 		private final String baseUri;
 		private final String rangeUri;
@@ -561,30 +560,29 @@ public class FauxPropertyDaoJena extends JenaBaseDao implements FauxPropertyDao
 				LockableOntModel lockableDisplayModel, String domainUri,
 				String baseUri, String rangeUri) {
 			try (LockedOntModel displayModel = lockableDisplayModel.read()) {
-				String queryString;
+				QueryHolder qHolder;
 				if (domainUri == null || domainUri.trim().isEmpty()
 						|| domainUri.equals(OWL.Thing.getURI())) {
-					queryString = bindValues(
-							QUERY_LOCATE_CONFIG_CONTEXT_WITH_NO_DOMAIN,
-							uriValue("baseUri", baseUri),
-							uriValue("rangeUri", rangeUri));
+					qHolder = queryHolder(
+							QUERY_LOCATE_CONFIG_CONTEXT_WITH_NO_DOMAIN)
+							.bindToUri("baseUri", baseUri).bindToUri(
+									"rangeUri", rangeUri);
 				} else {
-					queryString = bindValues(
-							QUERY_LOCATE_CONFIG_CONTEXT_WITH_DOMAIN,
-							uriValue("baseUri", baseUri),
-							uriValue("rangeUri", rangeUri),
-							uriValue("domainUri", domainUri));
+					qHolder = queryHolder(
+							QUERY_LOCATE_CONFIG_CONTEXT_WITH_DOMAIN)
+							.bindToUri("baseUri", baseUri)
+							.bindToUri("rangeUri", rangeUri)
+							.bindToUri("domainUri", domainUri);
 				}
 				if (log.isDebugEnabled()) {
 					log.debug("domainUri=" + domainUri + ", baseUri=" + baseUri
-							+ ", rangeUri=" + rangeUri + ", queryString="
-							+ queryString);
+							+ ", rangeUri=" + rangeUri + ", qHolder=" + qHolder);
 				}
 
 				ParserLocateConfigContext parser = new ParserLocateConfigContext(
 						domainUri, baseUri, rangeUri);
-				Set<ConfigContext> contexts = new SparqlQueryRunner(
-						displayModel).executeSelect(parser, queryString);
+				Set<ConfigContext> contexts = createSelectQueryContext(
+						displayModel, qHolder).execute().parse(parser);
 
 				log.debug("found " + contexts.size() + " contexts: " + contexts);
 				return contexts;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoJena.java

@@ -13,7 +13,7 @@ import java.util.List;
 import java.util.Random;
 import java.util.Set;
 
-import org.apache.commons.lang.NotImplementedException;
+import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -605,12 +605,12 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
 
     public Collection<String> getAllIndividualUris() {
         //this is implemented in IndivdiualSDB
-        throw new NotImplementedException();
+        throw new NotImplementedException("");
     }  
 
     public Iterator<String> getUpdatedSinceIterator(long updatedSince){
         //this is implemented in IndivdiualSDB
-        throw new NotImplementedException();
+        throw new NotImplementedException("");
     }
 
     public boolean isIndividualOfClass(String vclassURI, String indURI) {

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

@@ -13,7 +13,7 @@ import java.util.LinkedList;
 import java.util.List;
 
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.joda.time.DateTime;

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

@@ -868,6 +868,28 @@ public class JenaBaseDao extends JenaBaseDaoCon {
         return label;
     }
     
+    /**
+     * Searches for literal in preferred language.
+     * @param labels
+     * 				the literals to search; must not be null
+     * @return the literal in preferred language if its containing in given list; 
+     * otherwise the first entry will returned; returns null if an empty list was given 
+     */
+    protected Literal tryLiteralForPreferredLanguages(List<Literal> labels) {
+    	
+    	// search for literal of preferred language
+    	for (Literal literal : labels) {
+	    	for (String lang : PREFERRED_LANGUAGES) {
+	    		if (lang.equals(literal.getLanguage())) {
+	    			return literal;
+	    		}
+	    	}
+    	}
+
+    	// return first literal as last resort
+    	return 0 == labels.size() ? null : labels.get(0);
+    }
+    
     private Literal tryPropertyForPreferredLanguages( OntResource r, Property p, boolean alsoTryNoLang ) {
     	Literal label = null;
 	    List<RDFNode> labels = r.listPropertyValues(p).toList();
@@ -1149,7 +1171,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     	
     	String describeQueryStr =    "DESCRIBE <" + res.getURI() + ">" ;
     	
-//    	?	"PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n\n" +
+//    	?	"PREFIX afn: <http://jena.apache.org/ARQ/function#> \n\n" +
 //    		"DESCRIBE ?bnode \n" +
 //    	    "WHERE { \n" +
 //    		"    FILTER(afn:bnode(?bnode) = \"" + res.getId().toString() + "\")\n" +

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtils.java

@@ -262,7 +262,7 @@ public class JenaModelUtils {
         dataset.getLock().enterCriticalSection(Lock.READ);
         try {
             StringBuffer buff = new StringBuffer();
-            buff.append("PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n")
+            buff.append("PREFIX afn: <http://jena.apache.org/ARQ/function#> \n")
             .append("CONSTRUCT { \n")
             .append("  ?res <" + property.getURI() + "> ?o } WHERE { \n");
             if (graphURI != null) {
@@ -294,7 +294,7 @@ public class JenaModelUtils {
         
         StringBuffer describeQueryStrBuff = new StringBuffer() 
             .append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n")
-            .append("PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n")
+            .append("PREFIX afn: <http://jena.apache.org/ARQ/function#> \n")
             .append("DESCRIBE ?res WHERE { \n");
             if (graphURI != null) {
                 describeQueryStrBuff

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

@@ -11,7 +11,7 @@ import java.util.List;
 import java.util.Map;
 
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

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

@@ -7,16 +7,19 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Objects;
 import java.util.Set;
 
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntResource;
 import org.apache.jena.query.Dataset;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryExecution;
@@ -26,6 +29,7 @@ import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.QuerySolutionMap;
 import org.apache.jena.query.ResultSet;
 import org.apache.jena.query.Syntax;
+import org.apache.jena.rdf.model.Literal;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Property;
@@ -503,7 +507,8 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
             return Collections.emptyMap();
         }        
         
-        Map<String, String> types = new LinkedHashMap<String, String>();
+        Map<String, String> result = new LinkedHashMap<String, String>();
+        Map<String, List<Literal>> types = new LinkedHashMap<String, List<Literal>>();
         DatasetWrapper w = dwf.getDatasetWrapper();
         Dataset dataset = w.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);
@@ -521,16 +526,24 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
                 }
                 
                 RDFNode labelNode = soln.get("label");
-                String label = null;
-                if (labelNode.isLiteral()) {
-                    label = labelNode.asLiteral().getLexicalForm();
+                if (StringUtils.isNotBlank(type) && labelNode.isLiteral()) {
+                	
+                	List<Literal> langLabels = types.get(type);
+                	if (null == langLabels) {
+                		types.put(type, langLabels = new ArrayList<Literal>());
+                	}
+                	langLabels.add(labelNode.asLiteral());
+                    
+                }
             }
             
-                if (StringUtils.isNotBlank(type) && StringUtils.isNotBlank(label)) {
-                    types.put(type, label);
+            // choose labels corresponding to preferred languages
+            Set<Entry<String, List<Literal>>> typeEntries = types.entrySet();
+            for (Entry<String, List<Literal>> current : typeEntries) {
+            	result.put(current.getKey(), tryLiteralForPreferredLanguages(current.getValue()).getLexicalForm());
             }
-            }
-            return types;
+            
+            return result;
             
         } catch (Exception e) {
             log.error("Error getting most specific types for subject " + subjectUri);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/QueryUtils.java

@@ -9,8 +9,8 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.ObjectUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.ObjectUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceGraph.java

@@ -7,6 +7,7 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
+import java.util.function.Supplier;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -524,6 +525,16 @@ public class RDFServiceGraph implements GraphWithPerform {
             return null;
         }
 
+        @Override
+        public void execute(Runnable runnable) {
+
+        }
+
+        @Override
+        public <T> T calculate(Supplier<T> supplier) {
+            return null;
+        }
+
         @Override
         public boolean transactionsSupported() {
             return true;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/SparqlGraphMultilingual.java

@@ -8,7 +8,7 @@ import java.util.Comparator;
 import java.util.LinkedList;
 import java.util.List;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/VitroModelSource.java

@@ -3,7 +3,7 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import javax.servlet.ServletContext;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelReader;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/EditConfigurationVTwo.java

@@ -16,8 +16,8 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpSession;
 
 import org.apache.commons.fileupload.servlet.ServletFileUpload;
-import org.apache.commons.lang.builder.ToStringBuilder;
-import org.apache.commons.lang.builder.ToStringStyle;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.joda.time.DateTime;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/EditN3GeneratorVTwo.java

@@ -11,7 +11,7 @@ import java.util.Map;
 import java.util.Set;
 import java.util.regex.Matcher;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -68,7 +68,7 @@ public class EditN3GeneratorVTwo {
                 }
                 log.debug("The original value String is " + values.toString());                
                 
-                String valueString = org.apache.commons.lang.StringUtils.join(values,
+                String valueString = org.apache.commons.lang3.StringUtils.join(values,
                         ">, <");                                
                 valueString = "<" + valueString + ">";                
                 log.debug("The multiUri value String is " + valueString);
@@ -233,7 +233,7 @@ public class EditN3GeneratorVTwo {
                 log.debug("value of literal for " + var + " was null");        
         	}
         }
-        String valueString = org.apache.commons.lang.StringUtils.join(n3Values, ",");
+        String valueString = org.apache.commons.lang3.StringUtils.join(n3Values, ",");
         
         //Substitute it in to n3
         String varRegex = "\\?" + var + "(?=\\p{Punct}|\\p{Space}|$)";

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/MultiValueEditSubmission.java

@@ -11,9 +11,9 @@ import java.util.List;
 import java.util.Map;
 
 import org.apache.commons.fileupload.FileItem;
-import org.apache.commons.lang.StringUtils;
-import org.apache.commons.lang.builder.ToStringBuilder;
-import org.apache.commons.lang.builder.ToStringStyle;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.joda.time.format.DateTimeFormat;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/fields/ChildVClassesWithParent.java

@@ -7,7 +7,7 @@ import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import org.apache.jena.vocabulary.OWL;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/fields/FieldVTwo.java

@@ -5,8 +5,8 @@ package edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.commons.lang.builder.ToStringBuilder;
-import org.apache.commons.lang.builder.ToStringStyle;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
 
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.BaseEditElementVTwo;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditElementVTwo;

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

@@ -14,7 +14,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/BaseEditConfigurationGenerator.java

@@ -6,7 +6,7 @@ import java.util.List;
 
 import javax.servlet.http.HttpSession;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import org.apache.jena.ontology.OntModel;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DefaultAddMissingIndividualFormGenerator.java

@@ -11,7 +11,7 @@ import java.util.Map;
 import javax.servlet.http.HttpSession;
 
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.searchresult.IndividualSearchResult;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -226,7 +226,7 @@ public class DefaultAddMissingIndividualFormGenerator implements EditConfigurati
     	return prefixes;
     }
     
-    private String getN3ForName() {
+    protected String getN3ForName() {
     	return "?" + objectVarName + " rdfs:label ?name .";
     }
     

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/validators/AntiXssValidation.java

@@ -7,7 +7,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.owasp.validator.html.AntiSamy;
 import org.owasp.validator.html.CleanResults;
 import org.owasp.validator.html.PolicyException;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/validators/DefaultDataPropertyFormValidator.java

@@ -6,7 +6,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/controller/ProcessRdfFormController.java

@@ -8,7 +8,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filters/ModelSwitcher.java

@@ -15,7 +15,7 @@ import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames.DISPLAY_TB
 import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filters/StartupStatusDisplayFilter.java

@@ -18,7 +18,7 @@ import javax.servlet.ServletResponse;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;

api/src/main/java/edu/cornell/mannlib/vitro/webapp/filters/VitroURL.java

@@ -12,7 +12,7 @@ import java.util.List;
 import java.util.regex.Pattern;
 import java.util.regex.Matcher;
 
-import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/freemarker/config/FreemarkerConfiguration.java

@@ -13,7 +13,7 @@ import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 import javax.servlet.http.HttpServletRequest;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/freemarker/loader/FreemarkerTemplateLoader.java

@@ -18,7 +18,7 @@ import java.util.TreeSet;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/i18n/selection/LocaleSelectionController.java

@@ -11,8 +11,8 @@ import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.LocaleUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.LocaleUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/i18n/selection/LocaleSelectionSetup.java

@@ -10,8 +10,8 @@ import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 
-import org.apache.commons.lang.LocaleUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.LocaleUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
@@ -132,6 +132,12 @@ public class LocaleSelectionSetup implements ServletContextListener {
 
 	private Locale buildLocale(String localeString)
 			throws IllegalArgumentException {
+
+		// Replicate exception from lang2 with empty strings
+		if ("".equals(localeString)) {
+			throw new IllegalArgumentException("Invalid locale format");
+		}
+
 		Locale locale = LocaleUtils.toLocale(localeString);
 
 		if (!"es_GO".equals(localeString) && // No complaint about bogus locale

api/src/main/java/edu/cornell/mannlib/vitro/webapp/imageprocessor/imageio/IIOImageProcessor.java

@@ -2,7 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.imageprocessor.imageio;
 
-import com.sun.media.jai.codec.MemoryCacheSeekableStream;
 import edu.cornell.mannlib.vitro.webapp.modules.Application;
 import edu.cornell.mannlib.vitro.webapp.modules.ComponentStartupStatus;
 import edu.cornell.mannlib.vitro.webapp.modules.imageProcessor.ImageProcessor;
@@ -10,11 +9,8 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import javax.imageio.ImageIO;
-import javax.media.jai.JAI;
-import javax.media.jai.RenderedOp;
-import javax.media.jai.operator.BandSelectDescriptor;
-import javax.media.jai.operator.StreamDescriptor;
-import javax.media.jai.util.ImagingListener;
+import javax.imageio.stream.ImageInputStream;
+import javax.imageio.stream.MemoryCacheImageInputStream;
 import java.awt.geom.AffineTransform;
 import java.awt.image.AffineTransformOp;
 import java.awt.image.BufferedImage;
@@ -55,8 +51,8 @@ public class IIOImageProcessor implements ImageProcessor {
 	 */
 	@Override
 	public void startup(Application application, ComponentStartupStatus ss) {
-		JAI.getDefaultInstance().setImagingListener(
-				new NonNoisyImagingListener());
+//		JAI.getDefaultInstance().setImagingListener(
+//				new NonNoisyImagingListener());
 	}
 
 	@Override
@@ -66,7 +62,7 @@ public class IIOImageProcessor implements ImageProcessor {
 
 	@Override
 	public Dimensions getDimensions(InputStream imageStream) throws ImageProcessorException, IOException {
-		MemoryCacheSeekableStream stream = new MemoryCacheSeekableStream(imageStream);
+		ImageInputStream stream = new MemoryCacheImageInputStream(imageStream);
 		BufferedImage image = ImageIO.read(stream);
 		return new Dimensions(image.getWidth(), image.getHeight());
 	}
@@ -80,7 +76,7 @@ public class IIOImageProcessor implements ImageProcessor {
 			CropRectangle crop, Dimensions limits)
 			throws ImageProcessorException, IOException {
 		try {
-			MemoryCacheSeekableStream stream = new MemoryCacheSeekableStream(mainImageStream);
+			ImageInputStream stream = new MemoryCacheImageInputStream(mainImageStream);
 			BufferedImage mainImage = ImageIO.read(stream);
 
 			BufferedImage bufferedImage = new BufferedImage(mainImage.getWidth(), mainImage.getHeight(), BufferedImage.TYPE_3BYTE_BGR); // BufferedImage.TYPE_INT_RGB
@@ -176,33 +172,4 @@ public class IIOImageProcessor implements ImageProcessor {
 		ImageIO.write(image, "JPG", bytes);
 		return bytes.toByteArray();
 	}
-
-	/**
-	 * This ImagingListener means that Java Advanced Imaging won't dump an
-	 * exception log to System.out. It writes to the log, instead.
-	 * 
-	 * Further, since the lack of native accelerator classes isn't an error, it
-	 * is written as a simple log message.
-	 */
-	static class NonNoisyImagingListener implements ImagingListener {
-		@Override
-		public boolean errorOccurred(String message, Throwable thrown,
-				Object where, boolean isRetryable) throws RuntimeException {
-			if (thrown instanceof RuntimeException) {
-				throw (RuntimeException) thrown;
-			}
-			if ((thrown instanceof NoClassDefFoundError)
-					&& (thrown.getMessage()
-							.contains("com/sun/medialib/mlib/Image"))) {
-				log.info("Java Advanced Imaging: Could not find mediaLib "
-						+ "accelerator wrapper classes. "
-						+ "Continuing in pure Java mode.");
-				return false;
-			}
-			log.error(thrown, thrown);
-			return false;
-		}
-
-	}
-
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/imageprocessor/jai/JaiImageProcessor.java

@@ -2,234 +2,44 @@
 
 package edu.cornell.mannlib.vitro.webapp.imageprocessor.jai;
 
-import java.awt.geom.AffineTransform;
-import java.awt.image.AffineTransformOp;
-import java.awt.image.BufferedImage;
-import java.awt.image.ColorConvertOp;
-import java.awt.image.ColorModel;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-import javax.imageio.ImageIO;
-import javax.media.jai.JAI;
-import javax.media.jai.RenderedOp;
-import javax.media.jai.operator.BandSelectDescriptor;
-import javax.media.jai.operator.StreamDescriptor;
-import javax.media.jai.util.ImagingListener;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.sun.media.jai.codec.MemoryCacheSeekableStream;
-
+import edu.cornell.mannlib.vitro.webapp.imageprocessor.imageio.IIOImageProcessor;
 import edu.cornell.mannlib.vitro.webapp.modules.Application;
 import edu.cornell.mannlib.vitro.webapp.modules.ComponentStartupStatus;
 import edu.cornell.mannlib.vitro.webapp.modules.imageProcessor.ImageProcessor;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import java.io.IOException;
+import java.io.InputStream;
 
 /**
- * Crop the main image as specified, and scale it to the correct size for a
- * thumbnail.
+ * Re-implemented as ImageIO / TwelveMonkeys plugin for better OpenJDK compatibility and to remove
+ * JAI codec dependencies that are not distributed via Maven
  *
- * Use the JAI library to read the file because the javax.imageio package
- * doesn't read extended JPEG properly. Use JAI to remove transparency from
- * JPEGs and PNGs, simply by removing the alpha channel. Annoyingly, this will
- * not work with GIFs with transparent pixels.
- * 
- * The transforms in the JAI library are buggy, so standard AWT operations do
- * the scaling and cropping. The most obvious problem in the JAI library is the
- * refusal to crop after scaling an image.
- * 
- * Scale first to avoid the boundary error that produces black lines along the
- * edge of the image.
- * 
- * Use the javax.imagio pacakge to write the thumbnail image as a JPEG file.
+ * This transitional stub extends the new class, and logs warnings for people to update their config
  */
-public class JaiImageProcessor implements ImageProcessor {
+@Deprecated
+public class JaiImageProcessor extends IIOImageProcessor {
 	private static final Log log = LogFactory.getLog(JaiImageProcessor.class);
 
-	/** If an image has 3 color bands and 1 alpha band, we want these. */
-	private static final int[] COLOR_BAND_INDEXES = new int[] { 0, 1, 2 };
-
-	/**
-	 * Prevent Java Advanced Imaging from complaining about the lack of
-	 * accelerator classes.
-	 */
+	@Deprecated
 	@Override
 	public void startup(Application application, ComponentStartupStatus ss) {
-		JAI.getDefaultInstance().setImagingListener(
-				new NonNoisyImagingListener());
+		log.warn("JaiImageProcessor is deprecated and will be removed - please update config/applicationSetup.n3 to use edu.cornell.mannlib.vitro.webapp.imageprocessor.imageio.IIOImageProcessor");
+		super.startup(application, ss);
 	}
 
+	@Deprecated
 	@Override
-	public void shutdown(Application application) {
-		// Nothing to tear down.
+	public Dimensions getDimensions(InputStream imageStream) throws ImageProcessorException, IOException {
+		log.warn("JaiImageProcessor is deprecated and will be removed - please update config/applicationSetup.n3 to use edu.cornell.mannlib.vitro.webapp.imageprocessor.imageio.IIOImageProcessor");
+		return super.getDimensions(imageStream);
 	}
 
+	@Deprecated
 	@Override
-	public Dimensions getDimensions(InputStream imageStream)
-			throws ImageProcessorException, IOException {
-		MemoryCacheSeekableStream stream = new MemoryCacheSeekableStream(
-				imageStream);
-		RenderedOp image = JAI.create("stream", stream);
-		return new Dimensions(image.getWidth(), image.getHeight());
+	public InputStream cropAndScale(InputStream mainImageStream, CropRectangle crop, Dimensions limits) throws ImageProcessorException, IOException {
+		log.warn("JaiImageProcessor is deprecated and will be removed - please update config/applicationSetup.n3 to use edu.cornell.mannlib.vitro.webapp.imageprocessor.imageio.IIOImageProcessor");
+		return super.cropAndScale(mainImageStream, crop, limits);
 	}
-
-	/**
-	 * Crop the main image according to this rectangle, and scale it to the
-	 * correct size for a thumbnail.
-	 */
-	@Override
-	public InputStream cropAndScale(InputStream mainImageStream,
-			CropRectangle crop, Dimensions limits)
-			throws ImageProcessorException, IOException {
-		try {
-			RenderedOp mainImage = loadImage(mainImageStream);
-
-			BufferedImage bufferedImage = new BufferedImage(mainImage.getWidth(), mainImage.getHeight(), BufferedImage.TYPE_3BYTE_BGR); // BufferedImage.TYPE_INT_RGB
-			new ColorConvertOp(null).filter(mainImage.getAsBufferedImage(), bufferedImage);
-
-			log.debug("initial image: " + imageSize(bufferedImage));
-
-			log.debug("initial crop: " + crop);
-			CropRectangle boundedCrop = limitCropRectangleToImageBounds(
-					bufferedImage, crop);
-			log.debug("bounded crop: " + boundedCrop);
-
-			float scaleFactor = figureScaleFactor(boundedCrop, limits);
-			log.debug("scale factor: " + scaleFactor);
-
-			BufferedImage scaledImage = scaleImage(bufferedImage, scaleFactor);
-			log.debug("scaled image: " + imageSize(scaledImage));
-
-			CropRectangle rawScaledCrop = adjustCropRectangleToScaledImage(
-					boundedCrop, scaleFactor);
-			log.debug("scaled crop: " + rawScaledCrop);
-			CropRectangle scaledCrop = limitCropRectangleToImageBounds(
-					scaledImage, rawScaledCrop);
-			log.debug("bounded scaled crop: " + scaledCrop);
-
-			BufferedImage croppedImage = cropImage(scaledImage, scaledCrop);
-			log.debug("cropped image: " + imageSize(croppedImage));
-
-			byte[] jpegBytes = encodeAsJpeg(croppedImage);
-			return new ByteArrayInputStream(jpegBytes);
-		} catch (Exception e) {
-			throw new IllegalStateException("Failed to scale the image", e);
-		}
-	}
-
-	private RenderedOp loadImage(InputStream imageStream) {
-		return StreamDescriptor.create(new MemoryCacheSeekableStream(
-				imageStream), null, null);
-	}
-
-	private RenderedOp makeImageOpaque(RenderedOp image) {
-		ColorModel colorModel = image.getColorModel();
-
-		if (!colorModel.hasAlpha()) {
-			// The image is already opaque.
-			return image;
-		}
-
-		if (image.getNumBands() == 4) {
-				// The image has a separate alpha channel. Drop the alpha channel.
-			return BandSelectDescriptor.create(image, COLOR_BAND_INDEXES, null);
-		}
-
-		// Don't know how to handle it. Probably a GIF with a transparent
-		// background. Give up.
-		return image;
-	}
-
-	private String imageSize(BufferedImage image) {
-		return image.getWidth() + " by " + image.getHeight();
-	}
-
-	private CropRectangle limitCropRectangleToImageBounds(BufferedImage image,
-			CropRectangle crop) {
-
-		int imageWidth = image.getWidth();
-		int imageHeight = image.getHeight();
-
-		// Ensure that x and y are at least zero, but not big enough to push the
-		// crop rectangle out of the image.
-		int greatestX = imageWidth - MINIMUM_CROP_SIZE;
-		int greatestY = imageHeight - MINIMUM_CROP_SIZE;
-		int x = Math.max(0, Math.min(greatestX, Math.abs(crop.x)));
-		int y = Math.max(0, Math.min(greatestY, Math.abs(crop.y)));
-
-		// Ensure that width and height are at least as big as the minimum, but
-		// no so big as to extend beyond the image.
-		int greatestW = imageWidth - x;
-		int greatestH = imageHeight - y;
-		int w = Math.max(MINIMUM_CROP_SIZE, Math.min(greatestW, crop.width));
-		int h = Math.max(MINIMUM_CROP_SIZE, Math.min(greatestH, crop.height));
-
-		return new CropRectangle(x, y, h, w);
-	}
-
-	private float figureScaleFactor(CropRectangle boundedCrop, Dimensions limits) {
-		float horizontalScale = ((float) limits.width)
-				/ ((float) boundedCrop.width);
-		float verticalScale = ((float) limits.height)
-				/ ((float) boundedCrop.height);
-		return Math.min(horizontalScale, verticalScale);
-	}
-
-	private BufferedImage scaleImage(BufferedImage image, float scaleFactor) {
-		AffineTransform transform = AffineTransform.getScaleInstance(
-				scaleFactor, scaleFactor);
-		AffineTransformOp atoOp = new AffineTransformOp(transform, null);
-		return atoOp.filter(image, null);
-	}
-
-	private CropRectangle adjustCropRectangleToScaledImage(CropRectangle crop,
-			float scaleFactor) {
-		int newX = (int) (crop.x * scaleFactor);
-		int newY = (int) (crop.y * scaleFactor);
-		int newHeight = (int) (crop.height * scaleFactor);
-		int newWidth = (int) (crop.width * scaleFactor);
-		return new CropRectangle(newX, newY, newHeight, newWidth);
-	}
-
-	private BufferedImage cropImage(BufferedImage image, CropRectangle crop) {
-		return image.getSubimage(crop.x, crop.y, crop.width, crop.height);
-	}
-
-	private byte[] encodeAsJpeg(BufferedImage image) throws IOException {
-		ByteArrayOutputStream bytes = new ByteArrayOutputStream();
-		ImageIO.write(image, "JPG", bytes);
-		return bytes.toByteArray();
-	}
-
-	/**
-	 * This ImagingListener means that Java Advanced Imaging won't dump an
-	 * exception log to System.out. It writes to the log, instead.
-	 * 
-	 * Further, since the lack of native accelerator classes isn't an error, it
-	 * is written as a simple log message.
-	 */
-	static class NonNoisyImagingListener implements ImagingListener {
-		@Override
-		public boolean errorOccurred(String message, Throwable thrown,
-				Object where, boolean isRetryable) throws RuntimeException {
-			if (thrown instanceof RuntimeException) {
-				throw (RuntimeException) thrown;
-			}
-			if ((thrown instanceof NoClassDefFoundError)
-					&& (thrown.getMessage()
-							.contains("com/sun/medialib/mlib/Image"))) {
-				log.info("Java Advanced Imaging: Could not find mediaLib "
-						+ "accelerator wrapper classes. "
-						+ "Continuing in pure Java mode.");
-				return false;
-			}
-			log.error(thrown, thrown);
-			return false;
-		}
-
-	}
-
 }

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

@@ -5,14 +5,16 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVParser;
+import org.apache.commons.csv.CSVRecord;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.skife.csv.CSVReader;
-import org.skife.csv.SimpleReader;
 
 import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
 
@@ -35,7 +37,6 @@ public class OntologyChangeParser {
 		
 	/**
 	 * @param diffPath Diff path
-	 * @throws IOException 
 	 */
 	
 	@SuppressWarnings({ "unchecked", "null", "static-access" })
@@ -50,52 +51,53 @@ public class OntologyChangeParser {
 		String destinationURI = null;
 		StringTokenizer stArr = null; 
 		FileInputStream in = new FileInputStream(new File(diffPath));
-		CSVReader readFile = new SimpleReader();
-		readFile.setSeperator('\t');
 
-		List<String[]> rows = readFile.parse(in);
+		CSVParser readFile = new CSVParser(new InputStreamReader(in),
+				CSVFormat.DEFAULT.withRecordSeparator('\t'));
 
-		for(int rowNum = 0; rowNum < rows.size(); rowNum++){
-			
-			String[] cols = rows.get(rowNum);
-			if (cols.length != 5) {
-				logger.logError("Invalid PromptDiff data at row " + (rowNum + 1) 
-					   + ". Expected 5 columns; found " + cols.length );
+		int rowNum = 0;
+		for (CSVRecord record : readFile) {
+			rowNum++;
+			if (record.size() != 5) {
+				logger.logError("Invalid PromptDiff data at row " + (rowNum)
+					   + ". Expected 5 columns; found " + record.size() );
 			} else {
-		
+				String col = null;
 				changeObj = new AtomicOntologyChange();
 
-				if (cols[0] != null && cols[0].length() > 0) {
-					changeObj.setSourceURI(cols[0]);
+				col = record.get(0);
+				if (col != null && col.length() > 0) {
+					changeObj.setSourceURI(col);
 				}
 
-				if (cols[1] != null && cols[1].length() > 0) {
-					changeObj.setDestinationURI(cols[1]);
+				col = record.get(1);
+				if (col != null && col.length() > 0) {
+					changeObj.setDestinationURI(col);
 				}
 
-				if (cols[4] != null && cols[4].length() > 0) {
-                  changeObj.setNotes(cols[4]);
+				col = record.get(4);
+				if (col != null && col.length() > 0) {
+                  changeObj.setNotes(col);
                 }
 
-				if ("Yes".equals(cols[2])) {
+				if ("Yes".equals(record.get(2))) {
 					changeObj.setAtomicChangeType(AtomicChangeType.RENAME);
-				} else if ("Delete".equals(cols[3])) {
+				} else if ("Delete".equals(record.get(3))) {
 					changeObj.setAtomicChangeType(AtomicChangeType.DELETE); 
-				} else if ("Add".equals(cols[3])) {
+				} else if ("Add".equals(record.get(3))) {
 					changeObj.setAtomicChangeType(AtomicChangeType.ADD);
 				} else {
 					logger.logError("Invalid rename or change type data: '" +
-							cols[2] + " " + cols[3] + "'");
+							record.get(2) + " " + record.get(3) + "'");
 				}
 
-				
 			    log.debug(changeObj);
 				
 				changeObjects.add(changeObj);
-					
+			}
 		}
 
-		}
+		readFile.close();
 		
 		if (changeObjects.size() == 0) {
 			logger.log("No ABox updates are required.");

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/RDFService.java

@@ -8,6 +8,7 @@ import java.util.List;
 
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelChangedListener;
+import org.apache.jena.rdf.model.RDFNode;
 
 /**
  * Interface for API to write, read, and update Vitro's RDF store, with support 
@@ -249,6 +250,10 @@ public interface RDFService {
 	 */
 	public ChangeSet manufactureChangeSet();
 
+	public long countTriples(RDFNode subject, RDFNode predicate, RDFNode object) throws RDFServiceException;
+
+	public Model getTriples(RDFNode subject, RDFNode predicate, RDFNode object, long limit, long offset) throws RDFServiceException;
+		
 	/**
      * Frees any resources held by this RDFService object
      * 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/AbstractModelDecorator.java

@@ -10,6 +10,7 @@ import java.util.Calendar;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.function.Supplier;
 
 import org.apache.jena.datatypes.RDFDatatype;
 import org.apache.jena.graph.Graph;
@@ -1078,4 +1079,33 @@ public abstract class AbstractModelDecorator implements Model {
 		return inner.isClosed();
 	}
 
+	@Override
+	public Statement getRequiredProperty(Resource resource, Property property, String s) {
+		return inner.getRequiredProperty(resource, property, s);
+	}
+
+	@Override
+	public Statement getProperty(Resource resource, Property property, String s) {
+		return inner.getProperty(resource, property, s);
+	}
+
+	@Override
+	public void executeInTxn(Runnable runnable) {
+		inner.executeInTxn(runnable);
+	}
+
+	@Override
+	public <T> T calculateInTxn(Supplier<T> supplier) {
+		return inner.calculateInTxn(supplier);
+	}
+
+	@Override
+	public PrefixMapping clearNsPrefixMap() {
+		return inner.clearNsPrefixMap();
+	}
+
+	@Override
+	public int numPrefixes() {
+		return inner.numPrefixes();
+	}
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/AbstractOntModelDecorator.java

@@ -11,6 +11,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.function.Supplier;
 
 import org.apache.jena.datatypes.RDFDatatype;
 import org.apache.jena.graph.Graph;
@@ -1775,4 +1776,34 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	public Model writeAll(OutputStream out, String lang, String base) {
 		return inner.writeAll(out, lang, base);
 	}
+
+	@Override
+	public Statement getRequiredProperty(Resource resource, Property property, String s) {
+		return inner.getRequiredProperty(resource, property, s);
+	}
+
+	@Override
+	public Statement getProperty(Resource resource, Property property, String s) {
+		return inner.getProperty(resource, property, s);
+	}
+
+	@Override
+	public void executeInTxn(Runnable runnable) {
+		inner.executeInTxn(runnable);
+	}
+
+	@Override
+	public <T> T calculateInTxn(Supplier<T> supplier) {
+		return inner.calculateInTxn(supplier);
+	}
+
+	@Override
+	public PrefixMapping clearNsPrefixMap() {
+		return inner.clearNsPrefixMap();
+	}
+
+	@Override
+	public int numPrefixes() {
+		return inner.numPrefixes();
+	}
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/filter/LanguageFilteringRDFService.java

@@ -468,6 +468,16 @@ public class LanguageFilteringRDFService implements RDFService {
         return s.manufactureChangeSet();
     }
 
+    @Override
+    public long countTriples(RDFNode subject, RDFNode predicate, RDFNode object) throws RDFServiceException {
+        return s.countTriples(subject, predicate, object);
+    }
+
+    @Override
+    public Model getTriples(RDFNode subject, RDFNode predicate, RDFNode object, long limit, long offset) throws RDFServiceException {
+        return s.getTriples(subject, predicate, object, limit, offset);
+    }
+
     @Override
     public void close() {
         s.close();            

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceFactorySingle.java

@@ -16,6 +16,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
 import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
+import org.apache.jena.rdf.model.RDFNode;
 
 /**
  * An RDFServiceFactory that always returns the same RDFService object
@@ -192,6 +193,16 @@ public class RDFServiceFactorySingle implements RDFServiceFactory {
             return s.manufactureChangeSet();
         }
 
+        @Override
+        public long countTriples(RDFNode subject, RDFNode predicate, RDFNode object) throws RDFServiceException {
+            return s.countTriples(subject, predicate, object);
+        }
+
+        @Override
+        public Model getTriples(RDFNode subject, RDFNode predicate, RDFNode object, long limit, long offset) throws RDFServiceException {
+            return s.getTriples(subject, predicate, object, limit, offset);
+        }
+
         @Override
         public void close() {
             // Don't close s.  It's being used by everybody.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceImpl.java

@@ -12,18 +12,24 @@ import java.util.concurrent.CopyOnWriteArrayList;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import org.apache.jena.atlas.io.StringWriterI;
 import org.apache.jena.graph.Node;
 import org.apache.jena.graph.NodeFactory;
 import org.apache.jena.graph.Triple;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.query.QueryParseException;
+import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.Syntax;
+import org.apache.jena.rdf.model.Literal;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelChangedListener;
 import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.RDFNode;
 import org.apache.jena.rdf.model.Statement;
 import org.apache.jena.rdf.model.StmtIterator;
+import org.apache.jena.riot.out.NodeFormatter;
+import org.apache.jena.riot.out.NodeFormatterTTL;
 import org.apache.jena.vocabulary.RDF;
 
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
@@ -34,6 +40,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
 import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
+import org.vivoweb.linkeddatafragments.datasource.rdfservice.RDFServiceBasedRequestProcessorForTPFs;
 
 public abstract class RDFServiceImpl implements RDFService {
 	
@@ -341,4 +348,120 @@ public abstract class RDFServiceImpl implements RDFService {
 		return ToString.simpleName(this) + "[" + ToString.hashHex(this) + "]";
 	}
 
+    @Override
+    public long countTriples(RDFNode subject, RDFNode predicate, RDFNode object) throws RDFServiceException {
+        StringBuilder whereClause = new StringBuilder();
+        StringBuilder orderBy = new StringBuilder();
+
+        if ( subject != null ) {
+            appendNode(whereClause.append(' '), subject);
+        } else {
+            whereClause.append(" ?s");
+            orderBy.append(" ?s");
+        }
+
+        if ( predicate != null ) {
+            appendNode(whereClause.append(' '), predicate);
+        } else {
+            whereClause.append(" ?p");
+            orderBy.append(" ?p");
+        }
+
+        if ( object != null ) {
+            appendNode(whereClause.append(' '), object);
+        } else {
+            whereClause.append(" ?o");
+            orderBy.append(" ?o");
+        }
+
+        long estimate = -1;
+
+        StringBuilder count = new StringBuilder();
+        count.append("SELECT (COUNT(*) AS ?count) WHERE { ");
+        count.append(whereClause.toString());
+        count.append(" . ");
+        count.append(" }");
+        CountConsumer countConsumer = new CountConsumer();
+        this.sparqlSelectQuery(count.toString(), countConsumer);
+        return countConsumer.count;
+    }
+
+    @Override
+    public Model getTriples(RDFNode subject, RDFNode predicate, RDFNode object, long limit, long offset) throws RDFServiceException {
+        StringBuilder whereClause = new StringBuilder();
+        StringBuilder orderBy = new StringBuilder();
+
+        if ( subject != null ) {
+            appendNode(whereClause.append(' '), subject);
+        } else {
+            whereClause.append(" ?s");
+            orderBy.append(" ?s");
+        }
+
+        if ( predicate != null ) {
+            appendNode(whereClause.append(' '), predicate);
+        } else {
+            whereClause.append(" ?p");
+            orderBy.append(" ?p");
+        }
+
+        if ( object != null ) {
+            appendNode(whereClause.append(' '), object);
+        } else {
+            whereClause.append(" ?o");
+            orderBy.append(" ?o");
+        }
+
+        StringBuilder constructQuery = new StringBuilder();
+
+        constructQuery.append("CONSTRUCT { ");
+        constructQuery.append(whereClause.toString());
+        constructQuery.append(" } WHERE { ");
+        constructQuery.append(whereClause.toString()).append(" . ");
+        constructQuery.append(" }");
+
+        if (orderBy.length() > 0) {
+            constructQuery.append(" ORDER BY").append(orderBy.toString());
+        }
+
+        if (limit > 0) {
+            constructQuery.append(" LIMIT ").append(limit);
+        }
+
+        if (offset > 0) {
+            constructQuery.append(" OFFSET ").append(offset);
+        }
+
+        Model triples = ModelFactory.createDefaultModel();
+        this.sparqlConstructQuery(constructQuery.toString(), triples);
+
+        return triples;
+    }
+
+    private void appendNode(StringBuilder builder, RDFNode node) {
+        if (node.isLiteral()) {
+            builder.append(literalToString(node.asLiteral()));
+        } else if (node.isURIResource()) {
+            builder.append('<' + node.asResource().getURI() + '>');
+        }
+    }
+
+    private String literalToString(Literal l) {
+        StringWriterI sw = new StringWriterI();
+        NodeFormatter fmt = new NodeFormatterTTL(null, null);
+        fmt.formatLiteral(sw, l.asNode());
+        return sw.toString();
+    }
+
+    class CountConsumer extends ResultSetConsumer {
+        public long count = -1;
+
+        @Override
+        protected void processQuerySolution(QuerySolution qs) {
+            if (count == -1) {
+                Literal literal = qs.getLiteral("count");
+                count = literal.getLong();
+            }
+        }
+    }
 }

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

@@ -16,6 +16,9 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.apache.jena.query.QuerySolutionMap;
+import org.apache.jena.query.Syntax;
+import org.apache.jena.rdf.model.Literal;
 import org.apache.jena.riot.RDFDataMgr;
 import org.apache.log4j.lf5.util.StreamUtils;
 
@@ -612,6 +615,71 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
         return graph.isIsomorphicWith(fromTripleStoreModel);
     }
 
+    @Override
+    public long countTriples(RDFNode subject, RDFNode predicate, RDFNode object) throws RDFServiceException {
+        Query countQuery = QueryFactory.create("SELECT (COUNT(?s) AS ?count) WHERE { ?s ?p ?o } ORDER BY ?s ?p ?o", Syntax.syntaxSPARQL_11);
+        QuerySolutionMap map = new QuerySolutionMap();
+        if ( subject != null ) {
+            map.add("s", subject);
+        }
+        if ( predicate != null ) {
+            map.add("p", predicate);
+        }
+        if ( object != null ) {
+            map.add("o", object);
+        }
+
+        DatasetWrapper dw = getDatasetWrapper();
+        try {
+            Dataset d = dw.getDataset();
+            try (QueryExecution qexec = QueryExecutionFactory.create(countQuery, d, map)) {
+                ResultSet results = qexec.execSelect();
+                if (results.hasNext()) {
+                    QuerySolution soln = results.nextSolution() ;
+                    Literal literal = soln.getLiteral("count");
+                    return literal.getLong();
+                }
+            }
+        } finally {
+            dw.close();
+        }
+
+        return 0;
+    }
+
+    @Override
+    public Model getTriples(RDFNode subject, RDFNode predicate, RDFNode object, long limit, long offset) throws RDFServiceException {
+        Query query = QueryFactory.create("CONSTRUCT WHERE { ?s ?p ?o }", Syntax.syntaxSPARQL_11);
+        QuerySolutionMap map = new QuerySolutionMap();
+        if ( subject != null ) {
+            map.add("s", subject);
+        }
+        if ( predicate != null ) {
+            map.add("p", predicate);
+        }
+        if ( object != null ) {
+            map.add("o", object);
+        }
+
+        query.setOffset(offset);
+        query.setLimit(limit);
+
+        Model triples = ModelFactory.createDefaultModel();
+
+        DatasetWrapper dw = getDatasetWrapper();
+        try {
+            Dataset d = dw.getDataset();
+            try (QueryExecution qexec = QueryExecutionFactory.create(query, d, map)) {
+                qexec.execConstruct(triples);
+            }
+
+            return triples;
+        } finally {
+            dw.close();
+        }
+    }
+
+
     @Override
     public void close() {
         // nothing
@@ -620,5 +688,4 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
     protected QueryExecution createQueryExecution(String queryString, Query q, Dataset d) {
         return QueryExecutionFactory.create(q, d);
     }
-    
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/sdb/RDFServiceSDB.java

@@ -4,20 +4,34 @@ package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.sdb;
 
 import java.io.IOException;
 import java.sql.Connection;
+import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.sql.Statement;
 
 import javax.sql.DataSource;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import org.apache.jena.datatypes.RDFDatatype;
+import org.apache.jena.datatypes.TypeMapper;
+import org.apache.jena.datatypes.xsd.XSDDatatype;
+import org.apache.jena.graph.Node;
+import org.apache.jena.graph.NodeFactory;
+import org.apache.jena.graph.Triple;
 import org.apache.jena.query.Dataset;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryExecution;
 import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.RDFNode;
 import org.apache.jena.sdb.SDBFactory;
 import org.apache.jena.sdb.Store;
 import org.apache.jena.sdb.StoreDesc;
+import org.apache.jena.sdb.layout2.NodeLayout2;
+import org.apache.jena.sdb.layout2.ValueType;
 import org.apache.jena.sdb.sql.SDBConnection;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
@@ -28,6 +42,8 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena;
+import org.apache.jena.sdb.store.DatabaseType;
+import org.apache.jena.sdb.store.LayoutType;
 
 public class RDFServiceSDB extends RDFServiceJena implements RDFService {
 
@@ -148,6 +164,116 @@ public class RDFServiceSDB extends RDFServiceJena implements RDFService {
         // However, in recent Jena this turns out to be much slower than executing against the dataset directly
     }
 
+    @Override
+    public long countTriples(RDFNode subject, RDFNode predicate, RDFNode object) throws RDFServiceException {
+        if (LayoutType.LayoutTripleNodesHash.equals(storeDesc.getLayout())) {
+            if (DatabaseType.MySQL.equals(storeDesc.getDbType()) ||
+                DatabaseType.PostgreSQL.equals(storeDesc.getDbType())) {
+                SDBConnection sdbConn = getSDBConnection();
+                try {
+                    String whereClause = makeWhereClause(subject, predicate, object);
+                    Statement stmt = sdbConn.getSqlConnection().createStatement();
+                    ResultSet rs = stmt.executeQuery("SELECT count(DISTINCT s,p,o) AS tcount FROM Quads" + (StringUtils.isEmpty(whereClause) ? "" : " WHERE " + whereClause));
+                    try {
+                        while (rs.next()) {
+                            return rs.getLong("tcount");
+                        }
+                    } finally {
+                        rs.close();
+                    }
+                } catch (SQLException sqle) {
+                    throw new RDFServiceException("Unable to retrieve triples", sqle);
+                } finally {
+                    close(sdbConn);
+                }
+            }
+        } else {
+            return super.countTriples(subject, predicate, object);
+        }
+
+        return super.countTriples(subject, predicate, object);
+    }
+
+    @Override
+    public Model getTriples(RDFNode subject, RDFNode predicate, RDFNode object, long limit, long offset) throws RDFServiceException {
+        if (LayoutType.LayoutTripleNodesHash.equals(storeDesc.getLayout())) {
+            if (DatabaseType.MySQL.equals(storeDesc.getDbType()) ||
+                DatabaseType.PostgreSQL.equals(storeDesc.getDbType())) {
+                Model triples = ModelFactory.createDefaultModel();
+
+                SDBConnection sdbConn = getSDBConnection();
+                try {
+                    String whereClause = makeWhereClause(subject, predicate, object);
+                    Statement stmt = sdbConn.getSqlConnection().createStatement();
+                    ResultSet rs = stmt.executeQuery("SELECT \n" +
+                            "N1.lex      AS s_lex,\n" +
+                            "N1.lang     AS s_lang,\n" +
+                            "N1.datatype AS s_datatype,\n" +
+                            "N1.type     AS s_type,\n" +
+                            "N2.lex      AS p_lex,\n" +
+                            "N2.lang     AS p_lang,\n" +
+                            "N2.datatype AS p_datatype,\n" +
+                            "N2.type     AS p_type,\n" +
+                            "N3.lex      AS o_lex,\n" +
+                            "N3.lang     AS o_lang,\n" +
+                            "N3.datatype AS o_datatype,\n" +
+                            "N3.type     AS o_type\n" +
+                            "FROM\n" +
+                            "(SELECT DISTINCT s,p,o FROM Quads" +
+                            (StringUtils.isEmpty(whereClause) ? "" : " WHERE " + whereClause) +
+                            " ORDER BY s,p,o " +
+                            (limit > 0 ? "LIMIT " + limit : "") +
+                            (offset > 0 ? " OFFSET " + offset : "") + ") Q\n" +
+                            "LEFT OUTER JOIN\n" +
+                            "\tNodes AS N1\n" +
+                            "ON ( Q.s = N1.hash )\n" +
+                            "LEFT OUTER JOIN\n" +
+                            "\tNodes AS N2\n" +
+                            "ON ( Q.p = N2.hash )\n" +
+                            "LEFT OUTER JOIN\n" +
+                            "\tNodes AS N3\n" +
+                            "ON ( Q.o = N3.hash )");
+
+                    try {
+                        while (rs.next()) {
+                            Node subjectNode = makeNode(
+                                    rs.getString("s_lex"),
+                                    rs.getString("s_datatype"),
+                                    rs.getString("s_lang"),
+                                    ValueType.lookup(rs.getInt("s_type")));
+
+                            Node predicateNode = makeNode(
+                                    rs.getString("p_lex"),
+                                    rs.getString("p_datatype"),
+                                    rs.getString("p_lang"),
+                                    ValueType.lookup(rs.getInt("p_type")));
+
+                            Node objectNode = makeNode(
+                                    rs.getString("o_lex"),
+                                    rs.getString("o_datatype"),
+                                    rs.getString("o_lang"),
+                                    ValueType.lookup(rs.getInt("o_type")));
+
+                            triples.add(
+                                    triples.asStatement(Triple.create(subjectNode, predicateNode, objectNode))
+                            );
+                        }
+                    } finally {
+                        rs.close();
+                    }
+                } catch (SQLException sqle) {
+                    throw new RDFServiceException("Unable to retrieve triples", sqle);
+                } finally {
+                    close(sdbConn);
+                }
+
+                return triples;
+            }
+        }
+
+        return super.getTriples(subject, predicate, object, limit, offset);
+    }
+
     @Override
     public void close() {
         if (conn != null) {
@@ -159,4 +285,55 @@ public class RDFServiceSDB extends RDFServiceJena implements RDFService {
         }
     }
 
+    // Copied from Jena SQLBridge2
+    private static Node makeNode(String lex, String datatype, String lang, ValueType vType) {
+        switch(vType) {
+            case BNODE:
+                return NodeFactory.createBlankNode(lex);
+            case URI:
+                return NodeFactory.createURI(lex);
+            case STRING:
+                return NodeFactory.createLiteral(lex, lang);
+            case XSDSTRING:
+                return NodeFactory.createLiteral(lex, XSDDatatype.XSDstring);
+            case INTEGER:
+                return NodeFactory.createLiteral(lex, XSDDatatype.XSDinteger);
+            case DOUBLE:
+                return NodeFactory.createLiteral(lex, XSDDatatype.XSDdouble);
+            case DATETIME:
+                return NodeFactory.createLiteral(lex, XSDDatatype.XSDdateTime);
+            case OTHER:
+                RDFDatatype dt = TypeMapper.getInstance().getSafeTypeByName(datatype);
+                return NodeFactory.createLiteral(lex, dt);
+            default:
+                log.warn("Unrecognized: (" + lex + ", " + lang + ", " + vType + ")");
+                return NodeFactory.createLiteral("UNRECOGNIZED");
+        }
+    }
+
+    private String makeWhereClause(RDFNode subject, RDFNode predicate, RDFNode object) {
+        StringBuilder whereClause = new StringBuilder();
+        if (subject != null) {
+            if (whereClause.length() > 0) {
+                whereClause.append(" AND ");
+            }
+            whereClause.append("s=").append(NodeLayout2.hash(subject.asNode()));
+        }
+
+        if (predicate != null) {
+            if (whereClause.length() > 0) {
+                whereClause.append(" AND ");
+            }
+            whereClause.append("p=").append(NodeLayout2.hash(predicate.asNode()));
+        }
+
+        if (object != null) {
+            if (whereClause.length() > 0) {
+                whereClause.append(" AND ");
+            }
+            whereClause.append("o=").append(NodeLayout2.hash(object.asNode()));
+        }
+
+        return whereClause.length() > 0 ? whereClause.toString() : null;
+    }
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/logging/LoggingRDFService.java

@@ -14,6 +14,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
+import org.apache.jena.rdf.model.RDFNode;
 
 /**
  * This RDFService wrapper adds instrumentation to the time-consuming methods of
@@ -182,6 +183,16 @@ public class LoggingRDFService implements RDFService {
 		return innerService.manufactureChangeSet();
 	}
 
+	@Override
+	public long countTriples(RDFNode subject, RDFNode predicate, RDFNode object) throws RDFServiceException {
+		return innerService.countTriples(subject, predicate, object);
+	}
+
+	@Override
+	public Model getTriples(RDFNode subject, RDFNode predicate, RDFNode object, long limit, long offset) throws RDFServiceException {
+		return innerService.getTriples(subject, predicate, object, limit, offset);
+	}
+
 	@Override
 	public void close() {
 		innerService.close();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/logging/RDFServiceLogger.java

@@ -7,7 +7,7 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.regex.Pattern;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;