Improve output: distinguish between failed assertions (failures) and unexpected exceptions (errors), and print a filtered stack trace for any exception.

webapp/web/jenaIngest/connectDB.jsp

@@ -0,0 +1,30 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+    <h2>Connect to Jena Database</h2>
+
+    <form action="ingest" method="post">
+        <input type="hidden" name="action" value="connectDB"/>
+
+    
+	<input type="text" style="width:80%;" name="jdbcUrl" value="jdbc:mysql://localhost/"/>
+    <p>JDBC URL</p>
+ 
+    <input type="text" name="username"/>
+    <p>username</p>
+
+    <input type="password" name="password"/>
+    <p>password</p>
+
+
+		<input id="tripleStoreRDB" name="tripleStore" type="radio" checked="checked" value="RDB"/>
+			<label for="tripleStoreRDB">Jena RDB</label>
+		<input id="tripleStoreSDB" name="tripleStore" type="radio" value="SDB"/>
+			<label for="tripleStoreRDB">Jena SDB (hash layout)</label>
+
+    
+        <select name="dbType">
+            <option value="MySQL">MySQL</option>
+        </select>
+    <p>database type</p>
+
+    <input type="submit" value="Connect Database"/>

webapp/web/jenaIngest/createModel.jsp

@@ -0,0 +1,9 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+    <h2>Create New Model</h2>
+
+    <form style="margin-bottom:2ex;" action="ingest" method="post">
+        <input type="hidden" name="action" value="createModel"/>
+	Model name: <input type="text" size="32" name="modelName"/>
+        <input type="submit" name="submit" value="Create Model"/>
+    </form>

webapp/web/jenaIngest/csv2rdf.jsp

@@ -0,0 +1,66 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Convert CSV to RDF</h2>
+
+    <form action="ingest" method="get"i>
+        <input type="hidden" name="action" value="csv2rdf"/>
+
+	<p><input type="radio" name="separatorChar" value="comma" checked="checked"/> comma separated 
+	<input type="radio" name="separatorChar" value="tab"/> tab separated </p>
+
+    <input type="text" style="width:80%;" name="csvUrl"/>
+    <p>CSV file URL (e.g. "file:///")</p>
+
+    <input type="text" name="namespace"/>
+    <p>Namespace in which to generate resources</p>
+
+	<input type="text" name="tboxNamespace"/>
+    <p>Namespace in which to generate class and properties</p>
+
+<!-- 
+ <input type="checkbox" name="discardTbox"/> do not add TBox or RBox to result model
+-->
+
+    <input type="text" name="typeName"/>
+    <p>Class Name for Resources</p>
+
+    <select name="destinationModelName">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"><%=modelName%></option>
+        <%    
+    }
+%>    <option value="">(none)</option>
+    </select>
+    <p>Destination Model</p>
+
+   <select name="tboxDestinationModelName">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"><%=modelName%></option>
+        <%    
+    }
+%>    <option value="">(none)</option>
+    </select>
+    <p>Destination Model for TBox</p>
+
+    <input type="submit" value="Convert CSV"/>

webapp/web/jenaIngest/executeWorkflow.jsp

@@ -0,0 +1,46 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Execute RDF-Encoded Ingest Workflow</h2>
+
+    <form action="ingest" method="get"i>
+        <input type="hidden" name="action" value="executeWorkflow"/>
+
+    <h3>Workflow</h3>
+   
+        <select name="workflowURI">
+             
+        <%
+              OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
+              jenaOntModel.enterCriticalSection(Lock.READ);
+              try {
+                  List savedQueries = (List) request.getAttribute("workflows");
+	          for (Iterator it = savedQueries.iterator(); it.hasNext();)  {
+	              Individual savedQuery = (Individual) it.next();
+                      String queryURI = savedQuery.getURI();
+                      String queryLabel = savedQuery.getLabel(null);
+                      %> <option value="<%=queryURI%>"><%=queryLabel%></option> <%
+                  }
+              } finally {
+                  jenaOntModel.leaveCriticalSection();
+	      }
+        %>
+        </select>
+  
+    <input type="submit" value="Next &gt;"/>

webapp/web/jenaIngest/exportSelection.jsp

@@ -0,0 +1,36 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<div class="staticPageBackground">
+
+<h2> Export to RDF </h2>
+
+<form action="" method="get">
+
+<ul>
+    <li style="list-style-type:none;"><input type="radio" name="subgraph" checked="checked" value="full"/> Export entire RDF model (including application metadata)</li>
+    <li style="list-style-type:none;"><input type="radio" name="subgraph" value="tbox"/> Export ontology/ontologies (TBox)</li>
+    <li style="list-style-type:none;"><input type="radio" name="subgraph" value="abox"/> Export instance data (ABox)</li>
+</ul>
+
+<hr/>
+
+<ul>
+    <li style="list-style-type:none;"><input type="radio" name="assertedOrInferred" checked="checked" value="asserted"/> Export only asserted statements </li>
+    <li style="list-style-type:none;"><input type="radio" name="assertedOrInferred" value="inferred"/> Export only inferred statements </li>
+    <li style="list-style-type:none;"><input type="radio" name="assertedOrInferred" value="full"/> Export asserted and inferred statements together </li>
+</ul>
+
+<h3>Select format</h3>
+<select name="format">
+    <option value="RDF/XML">RDF/XML</option>
+    <option value="RDF/XML-ABBREV">RDF/XML abbrev.</option>
+    <option value="N3">N3</option>
+    <option value="N-TRIPLES">N-Triples</option>
+    <option value="TURTLE">Turtle</option>
+</select>
+
+<input type="submit" name="submit" value="Export"/>
+
+</form>
+
+</div>

webapp/web/jenaIngest/generateTBox.jsp

@@ -0,0 +1,53 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Generate TBox from Assertions Data</h2>
+
+    <form action="ingest" method="get">
+        <input type="hidden" name="action" value="generateTBox"/>
+
+    <h3>Select Source Models for Assertions Data</h3>
+
+    <ul>
+		  <li><input type="checkbox" name="sourceModelName" value="vitro:jenaOntModel"/>webapp model</li>
+		  <li><input type="checkbox" name="sourceModelName" value="vitro:baseOntModel"/>webapp assertions</li>
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <li> <input type="checkbox" name="sourceModelName" value="<%=modelName%>"/><%=modelName%></li>
+        <%    
+    }
+%>
+    </ul>
+
+    <h3>Select Destination Model for Generated TBox</h3>
+
+    <select name="destinationModelName">
+           <option value="vitro:jenaOntModel"/>webapp model</option>
+           <option value="vitro:baseOntModel"/>webapp assertions</option>
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"/><%=modelName%></option>
+        <%    
+    }
+%>   
+    </select>
+
+    <input type="submit" value="Generate TBox"/>

webapp/web/jenaIngest/ingestMenu.jsp

@@ -0,0 +1,20 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<h2>Ingest Menu</h2>
+
+<ul>
+    <li><a href="ingest?action=connectDB">Connect DB</a></li>
+    <li><a href="ingest?action=listModels">Manage Jena Models</a></li>
+    <li><a href="ingest?action=subtractModels">Subtract One Model from Another</a></li>
+    <li><a href="ingest?action=csv2rdf">Convert CSV to RDF</a></li>
+    <li><a href="jenaXmlFileUpload">Load XML and convert to RDF</a></li>
+    <li><a href="ingest?action=renameBNodes">Name Blank Nodes</a></li>
+    <li><a href="ingest?action=smushSingleModel">Smush Resources</a></li>
+    <li><a href="ingest?action=generateTBox">Generate TBox</a></li>
+    <li><a href="ingest?action=executeSparql">Execute SPARQL CONSTRUCT</a></li>
+    <li><a href="ingest?action=processStrings">Process Property Value Strings</a></li>
+	<li><a href="ingest?action=splitPropertyValues">Split Property Value Strings into Multiple Property Values</a></li>
+	<li><a href="ingest?action=executeWorkflow">Execute Workflow</a></li> 
+</ul>
+
+

webapp/web/jenaIngest/listModels.jsp

@@ -0,0 +1,89 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.net.URLEncoder" %>
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+	maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <p><a href="ingest">Ingest Home</a></p>
+
+    <h2>Available Jena Models</h2>
+
+    <form action="ingest" method="get">
+        <input type="hidden" name="action" value="createModel"/>
+        <input type="submit" name="submit" value="Create Model"/>
+    </form>
+
+    <ul>
+
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <li style="padding-bottom:2em;padding-top:2em;"> <%=modelName%>
+            <table style="margin-left:2em;"><tr>
+            <td>
+            <form action="ingest" method="get">
+                <input type="hidden" name="action" value="loadRDFData"/>
+                <input type="hidden" name="modelName" value="<%=modelName%>"/>
+                <input type="submit" name="submit" value="load RDF data"/>
+            </form>
+            </td>
+            <td>
+            <c:url var="outputModelURL" value="ingest">
+            	<c:param name="action" value="outputModel"/>
+            	<c:param name="modelName" value="<%=modelName%>"/>
+            </c:url>
+            <a href="${outputModelURL}">output model</a>
+            </td>
+            <td>
+            <form action="ingest" method="post">
+                <input type="hidden" name="action" value="clearModel"/>
+                <input type="hidden" name="modelName" value="<%=modelName%>"/>
+                <input type="submit" name="submit" value="clear statements"/>
+            </form>
+            </td>
+            <td>
+            <form action="ingest" method="post">
+                <input type="hidden" name="action" value="removeModel"/>
+                <input type="hidden" name="modelName" value="<%=modelName%>"/>
+                <input type="submit" name="submit" value="remove"/>
+            </form>
+            </td>
+            </tr>
+            <tr>
+            <td>
+            <form action="ingest" method="post">
+                <input type="hidden" name="action" value="setWriteLayer"/>
+                <input type="hidden" name="modelName" value="<%=modelName%>"/>
+                <input type="submit" name="submit" value="set as current write layer"/>
+            </form>
+            <td>
+            <form action="ingest" method="post">
+                <input type="hidden" name="action" value="attachModel"/>
+                <input type="hidden" name="modelName" value="<%=modelName%>"/>
+                <input type="submit" name="submit" value="attach to webapp"/>
+            </form>
+            </td>
+            <td>
+            <form action="ingest" method="post">
+                <input type="hidden" name="action" value="detachModel"/>
+                <input type="hidden" name="modelName" value="<%=modelName%>"/>
+                <input type="submit" name="submit" value="detach from webapp"/>
+            </form>
+            </td>
+            <td>&nbsp;</td>
+            </tr>
+            </table>
+        </li> <%    
+    }
+%>
+    </ul>

webapp/web/jenaIngest/loadRDFData.jsp

@@ -0,0 +1,21 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+    <h2>Load RDF Data</h2>
+
+    <form style="margin-bottom:2ex;" action="ingest" method="post">
+    	<input type="hidden" name="modelName" value="<%=request.getParameter("modelName")%>"/>
+	<input type="hidden" name="action" value="loadRDFData"/>
+	<p>RDF document URI: <input type="text" size="32" name="docLoc"/></p>
+	<p>Or local filesystem path: <input type="text" size="32" name="filePath"/>
+	(If a directory is supplied, will attempt to load all files therein)</p>
+	<p>    
+        <select name="language">
+        	<option value="RDF/XML">RDF/XML</option>
+        	<option value="N3">N3</option>
+        	<option	value="N-TRIPLE">N-Triples</option>
+            <option value="TTL">Turtle</option>
+        </select>
+		<input type="submit" name="submit" value="Load Data"/>
+	</p>
+	
+    </form>

webapp/web/jenaIngest/processStrings.jsp

@@ -0,0 +1,73 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Process Property Value Strings</h2>
+
+    <form action="ingest" method="get"i>
+        <input type="hidden" name="action" value="processStrings"/>
+
+    <input type="text" style="width:80%;" name="className"/>
+    <p>String processor class</p>
+    
+    <input type="text" name="methodName"/>
+    <p>String processor method</p>
+
+    <input type="text" name="propertyName"/>
+    <p>Property URI</p>
+
+    <input type="text" name="newPropertyName"/>
+    <p>New Property URI</p>
+
+    <select name="destinationModelName">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"/><%=modelName%></option>
+        <%    
+    }
+%>   
+    </select>
+    <input type="checkbox" name="processModel" value="TRUE"/> apply changes directly to this model
+    <p>model to use</p>
+   
+    <select name="additionsModel">
+		<option value="">none</option>
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"><%=modelName%></option>
+        <%    
+    }
+%>   
+	</select>
+    <p>model in which to save added statements</p>
+
+    <select name="retractionsModel">
+		<option value="">none</option>
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"><%=modelName%></option>
+        <%    
+    }
+%>   
+	</select>
+    <p>model in which to save retracted statements</p>
+
+    <input type="submit" value="Process property values"/>

webapp/web/jenaIngest/renameBNodes.jsp

@@ -0,0 +1,57 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Convert Blank Nodes to Named Resources</h2>
+
+    <form action="ingest" method="get"i>
+        <input type="hidden" name="action" value="renameBNodes"/>
+
+    <h3>Select URI prefix</h3>
+   
+	<p>URIs will be constructed from the following string concatenated with a random integer:</p>
+	<input type="text" name="namespaceEtcStr"/> 
+
+    <p/>
+
+    <h3>Select Source Models</h3>
+
+    <ul>
+
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <li> <input type="checkbox" name="sourceModelName" value="<%=modelName%>"/><%=modelName%></li>
+        <%    
+    }
+%>
+    </ul>
+
+    <h3>Select Destination Model</h3>
+
+    <select name="destinationModelName">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"/><%=modelName%></option>
+        <%    
+    }
+%>   
+    </select>
+
+    <input type="submit" value="Rename Blank Nodes"/>

webapp/web/jenaIngest/smushSingleModel.jsp

@@ -0,0 +1,53 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Smush Resources</h2>
+
+    <form action="ingest" method="get"i>
+        <input type="hidden" name="action" value="smushSingleModel"/>
+
+    <h3>URI of Property with which To Smush
+	<input type="text" name="propertyURI"/> 
+
+    <h3>Select Source Models</h3>
+
+    <ul>
+
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <li> <input type="checkbox" name="sourceModelName" value="<%=modelName%>"/><%=modelName%></li>
+        <%    
+    }
+%>
+    </ul>
+
+    <h3>Select Destination Model</h3>
+
+    <select name="destinationModelName">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"/><%=modelName%></option>
+        <%    
+    }
+%>   
+    </select>
+
+    <input type="submit" value="Smush Resources"/>

webapp/web/jenaIngest/sparqlConstruct.jsp

@@ -0,0 +1,166 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    
+<%@page import="java.util.HashSet"%>
+<%@page import="java.util.Set"%>
+<%@page import="java.util.Arrays"%>
+<%@page import="java.util.ArrayList"%><h2>Execute SPARQL CONSTRUCT Query</h2>
+
+    <p><a href="ingest">Ingest Home</a></p>
+
+    <c:if test="${requestScope.constructedStmtCount != null}">
+        <h3 class="notice">${requestScope.constructedStmtCount} statements CONSTRUCTed</h3>
+    </c:if>
+
+    <c:if test="${errorMsg != null}"> 
+        <h3 class="error">${requestScope.errorMsg}</h3>
+    </c:if>
+
+    <c:if test="${requestScope.validationMessage != null}">
+        <h3 class="notice">${requestScope.validationMessage}</h3>
+    </c:if>
+
+    <form action="ingest" method="post">
+        <input type="hidden" name="action" value="executeSparql"/>
+
+    <h3>SPARQL Query
+   
+        <select name="savedQuery">
+             <option value="">select saved query</option>
+        <%
+              OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
+              jenaOntModel.enterCriticalSection(Lock.READ);
+              try {
+                  List savedQueries = (List) request.getAttribute("savedQueries");
+	          for (Iterator it = savedQueries.iterator(); it.hasNext();)  {
+	              Individual savedQuery = (Individual) it.next();
+                      String queryURI = savedQuery.getURI();
+                      String queryLabel = savedQuery.getLabel(null);
+                      %> <option value="<%=queryURI%>"><%=queryLabel%></option> <%
+                  }
+              } finally {
+                  jenaOntModel.leaveCriticalSection();
+	      }
+        %>
+        </select>
+  
+        <textarea rows="16" cols="40" name="sparqlQueryStr"><c:choose>
+    <c:when test="${param.sparqlQueryStr != null}">
+        ${param.sparqlQueryStr}
+    </c:when>
+    <c:otherwise>
+PREFIX rdf:   &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
+PREFIX rdfs:  &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
+PREFIX owl:   &lt;http://www.w3.org/2002/07/owl#&gt;
+PREFIX xsd:   &lt;http://www.w3.org/2001/XMLSchema#&gt;
+PREFIX vitro: &lt;http://vitro.mannlib.cornell.edu/ns/vitro/0.7#&gt;
+</c:otherwise>
+</c:choose>
+
+
+</textarea>
+
+    <h3>Select Source Models</h3>
+
+    <ul>
+<%
+	List<String> sourceModelNameList = new ArrayList<String>();
+	String[] sourceModelParamVals = request.getParameterValues("sourceModelName");
+	if (sourceModelParamVals != null) {
+	    sourceModelNameList.addAll(Arrays.asList(sourceModelParamVals));
+	}
+%>
+
+		  <li><input type="checkbox" name="sourceModelName" value="vitro:jenaOntModel"
+                    <%
+                        if (sourceModelNameList.contains("vitro:jenaOntModel")) {
+                        	%>checked="checked"<%
+                        }
+                    %>
+               />webapp model</li>
+		  <li><input type="checkbox" name="sourceModelName" value="vitro:baseOntModel"
+                    <%
+                        if (sourceModelNameList.contains("vitro:baseOntModel")) {
+                            %>checked="checked"<%
+                        }
+                    %>
+               />webapp assertions</li>
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <li> <input type="checkbox" name="sourceModelName" value="<%=modelName%>"
+                    <%
+                        if (sourceModelNameList.contains(modelName)) {
+                        	%> checked="checked" <%
+                        }
+                    %>
+                /><%=modelName%></li>
+        <%    
+    }
+%>
+    </ul>
+
+    <h3>Select Destination Model</h3>
+
+    <select name="destinationModelName">
+           <option value="vitro:jenaOntModel"
+              <% if ("vitro:jenaOntModel".equals(request.getParameter("destinationModelName"))) {
+            	  %> selected="selected" <%
+            	 }
+              %>
+            />webapp model</option>
+           <option value="vitro:baseOntModel"
+              <% if ("vitro:baseOntModel".equals(request.getParameter("destinationModelName"))) {
+                  %> selected="selected" <%
+                 }
+              %>
+            />webapp assertions</option>
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+    String modelName = (String) it.next();
+        %> <option value="<%=modelName%>" 
+                <%
+                 if (modelName.equals(request.getParameter("destinationModelName"))) {
+                     %> selected="selected" <%
+                 }
+                %>
+           /><%=modelName%></option>
+        <%    
+    }
+%>   
+    </select>
+
+    <c:choose>
+	    <c:when test="${paramValues['reasoning'] != null}">
+	        <c:forEach var="paramValue" items="${paramValues['reasoning']}">
+	            <c:if test="${paramValue eq 'pellet'}">
+	                <p><input type="checkbox" name="reasoning" value="pellet" checked="checked"/> include pellet reasoning </p>
+	            </c:if>
+	        </c:forEach>
+	    </c:when>
+        <c:otherwise>
+                    <p><input type="checkbox" name="reasoning" value="pellet" /> include Pellet OWL-DL reasoning </p>
+        </c:otherwise>
+    </c:choose>
+
+    <input type="submit" value="Execute CONSTRUCT"/>
+           

webapp/web/jenaIngest/splitPropertyValues.jsp

@@ -0,0 +1,65 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Split Property Value Strings into Multiple Property Values</h2>
+
+    <form action="ingest" method="get">
+        <input type="hidden" name="action" value="splitPropertyValues"/>
+    <h3>Select Source Models</h3>
+    <ul>
+		  <li><input type="checkbox" name="sourceModelName" value="vitro:jenaOntModel"/>webapp model</li>
+		  <li><input type="checkbox" name="sourceModelName" value="vitro:baseOntModel"/>webapp assertions</li>
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <li> <input type="checkbox" name="sourceModelName" value="<%=modelName%>"/><%=modelName%></li>
+        <%    
+    }
+%>
+    </ul>
+
+	
+	<input type="text" name="propertyURI"/>
+    <p>Property URI for which Values Should Be Split</p>	
+
+	<input type="text" name="splitRegex"/>
+    <p>Regex Pattern on which To Split</p>
+	
+	<input type="text" name="newPropertyURI"/>
+    <p>Property URI To Be Used with the Newly-Split Values</p>
+	
+	<h3></h3>
+	
+	<p>
+	<input type="checkbox" name="trim" value="true"/> trim bordering whitespace
+	</p>
+	
+    <h3>Select Destination Model</h3>
+
+    <select name="destinationModelName">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"/><%=modelName%></option>
+        <%    
+    }
+%>   
+    </select>
+
+    <input type="submit" value="Split Values"/>

webapp/web/jenaIngest/subtractModels.jsp

@@ -0,0 +1,58 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Subtract One Model from Another</h2>
+
+    <form action="ingest" method="get"i>
+        <input type="hidden" name="action" value="subtractModels"/>
+
+    <select name="modela">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"/><%=modelName%></option>
+        <%    
+    }
+%>   
+    </select>
+    <p>model to be subtracted from</p>
+
+    <select name="modelb">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"><%=modelName%></option>
+        <%    
+    }
+%>   
+	</select>
+    <p>model to subtract</p>
+
+    <select name="destinationModelName">
+<%
+    for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();
+        %> <option value="<%=modelName%>"><%=modelName%></option>
+        <%    
+    }
+%>   
+	</select>
+    <p>model in which difference should be saved</p>
+
+    <input type="submit" value="Subtract models"/>

webapp/web/jenaIngest/workflowStep.jsp

@@ -0,0 +1,49 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.ontology.Individual" %>
+<%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="com.hp.hpl.jena.shared.Lock" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.util.List" %>
+<%@ page import="java.net.URLEncoder" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <h2>Execute RDF-Encoded Ingest Workflow</h2>
+
+    <form action="ingest" method="get"i>
+        <input type="hidden" name="action" value="executeWorkflow"/>
+
+    <h3>Choose a Workflow Step at Which To Start</h3>
+   
+        <input type="hidden" name="workflowURI" value="${param.workflowURI}"/>
+
+		<select name="workflowStepURI">
+             
+        <%
+              OntModel jenaOntModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
+              jenaOntModel.enterCriticalSection(Lock.READ);
+              try {
+                  List workflowSteps  = (List) request.getAttribute("workflowSteps");
+	          for (Iterator it = workflowSteps.iterator(); it.hasNext();)  {
+	              Individual workflowStep = (Individual) it.next();
+                      String workflowStepURI = workflowStep.getURI();
+                      String workflowStepLabel = workflowStep.getLabel(null);
+					  String workflowStepString = (workflowStepLabel != null) ? workflowStepLabel : workflowStepURI;
+                      %> <option value="<%=workflowStepURI%>"><%=workflowStepString%></option> <%
+                  }
+              } finally {
+                  jenaOntModel.leaveCriticalSection();
+	      }
+        %>
+        </select>
+  
+    <input type="submit" value="Execute Workflow"/>

webapp/web/jenaIngest/xmlFileUpload.jsp

@@ -0,0 +1,33 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.net.URLEncoder" %>
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c" %>
+
+<%
+
+    ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
+    if (maker == null) {
+		maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+    }
+
+%>
+
+    <p><a href="ingest">Ingest Home</a></p>
+    
+
+    <form action="jenaXmlFileUpload" method="post" enctype="multipart/form-data">
+    
+    <input type="file" name="xmlfile"/>
+    
+	<select name="targetModel">
+
+<%  for (Iterator it = maker.listModels(); it.hasNext(); ) {
+	String modelName = (String) it.next();        %> 
+	  <option value="<%=modelName%>"><%= modelName %></option>                
+<% } %>
+        </select>
+        <input type="submit" name="submit" value="upload XML and convert to RDF"/>
+    </form>
+    

webapp/web/jenaIngest/xmlFileUploadSuccess.jsp

@@ -0,0 +1,17 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
+<%@ page import="java.util.Iterator" %>
+<%@ page import="java.net.URLEncoder" %>
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c" %>
+
+<%
+  
+
+%>
+<p>Uploaded XML files and converted to RDF.</p>
+<p>Loaded <%= request.getAttribute("statementCount") %> statements to the model <%= request.getAttribute("targetModel") %>.</p>
+
+<p><a href="ingest">Ingest Home</a></p>
+       
+