NIHVIVO-3130 NIHVIVO-3089 ingest tools fixes and improvements

webapp/web/jenaIngest/csv2rdf.jsp

@@ -17,7 +17,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>
@@ -36,15 +36,27 @@
     <p>Or upload a file from your computer:</p>
     <p><input type="file" name="filePath" /></p>
 
+    <p/>
+    <p>This tool will automatically generate a mini ontology to represent the 
+    data in the CSV file.  A property will be produced for each column in the 
+    spreadsheet, based on the text in the header for that column.</p><p>In what 
+    namespace should these properties be created?</p>
 	<input type="text" name="tboxNamespace"/>
-    <p>Namespace in which to generate class and properties</p>
+    <p>Namespace in which to generate properties</p>
 
 <!-- 
  <input type="checkbox" name="discardTbox"/> do not add TBox or RBox to result model
 -->
 
+    <p>
+    <p>Each row in the spreadsheet will produce an resource.  Each of these
+    resources will be a member of a class in the namespace selected above.</p>  
+    <p>What should the local name of this class be? This is normally a word or two 
+    in "camel case" starting with an uppercase letter.  (For example, if the 
+    spreadsheet represents a list of faculty members, you might enter 
+    "FacultyMember" on the next line.)</p> 
     <input type="text" name="typeName"/>
-    <p>Class Name for Resources</p>
+    <p>Class Local Name for Resources</p>
 
     <select name="destinationModelName">
         <option value="vitro:baseOntModel">webapp assertions</option>
@@ -56,7 +68,7 @@
     }
 %>    <option value="">(none)</option>
     </select>
-    <p>Destination Model</p>
+    <p>Model in which to save the converted spreadsheet data</p>
 
    <select name="tboxDestinationModelName">
         <option value="vitro:baseOntModel">webapp assertions</option>
@@ -68,6 +80,11 @@
     }
 %>    <option value="">(none)</option>
     </select>
-    <p>Destination Model for TBox</p>
+    <p>Model in which to save the automatically-generated ontology</p>
+
+    <p/>
+    <p>The data in the CSV file will initially be represented using blank
+    nodes (RDF resources without URIs).  You will choose how to assign
+    URIs to these resources in the next step.</p>
 
     <input class="submit" type="submit" value="Next Step"/>

webapp/web/jenaIngest/csv2rdfSelectUri.jsp

@@ -1,5 +1,8 @@
 <%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
 
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%>
+<%@ taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
+
 <%@ 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" %>
@@ -13,8 +16,7 @@
 <%@ page import="java.util.Set" %>
 <%@ page import="java.util.Map.Entry" %>
 
-<%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
-<%@page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %>
+<%@ page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %>
 <% request.setAttribute("requestedActions", new UseAdvancedDataToolsPages()); %>
 <vitro:confirmAuthorization />
 
@@ -22,7 +24,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>
@@ -46,16 +48,18 @@ function disableProperties(){
 
     <h3>Select URI prefix</h3>
    
-	<p>URIs will be constructed from the following string:</p>
+	<p>URIs will be constructed using the following base string:</p>
 	<input id="namespace" type="text" style="width:65%;" name="namespaceEtcStr"/> 
 
     <p/>
     
-    <p>You can concatenate above string with random integer OR your own pattern based on <b>values</b> of one of the properties (Properties will be enabled in the dropdown) </p>
+    <p>Each resource will be assigned a URI by taking the above string and 
+     adding either a random integer, or a string based on the value of one of the
+     the properties of the resource</p>
     
-    <input type="radio" value="integer" name="concatenate" checked="checked" onclick="disableProperties()"><b>No</b>, concatenate with random integer</input>
+    <input type="radio" value="integer" name="concatenate" checked="checked" onclick="disableProperties()">Use random integer</input>
     <br></br>
-    <input type="radio" value="pattern" name="concatenate" onclick="selectProperties()"><b>Yes</b>, concatenate with my pattern</input> 
+    <input type="radio" value="pattern" name="concatenate" onclick="selectProperties()">Use pattern based on values of </input> 
   
     
     <% Map<String,LinkedList<String>> propertyMap = (Map) request.getAttribute("propertyMap");
@@ -75,12 +79,16 @@ function disableProperties(){
     %>
     </select>
     <br></br>
-    <p>Enter your pattern that will prefix property value with an underscore eg. depID_$$$ where depID is your pattern and $$$ is the property value.</p>
+    <p>Enter a pattern using $$$ as the placeholder for the value of the property selected above.</p>
+    <p>For example, entering dept_$$$ might generate URIs with endings such as dept_Art or dept_Classics.</p>
     <input id="pattern" disabled="disabled" type="text" style="width:35%;" name="pattern"/> 
     
-    <%String modelName = (String) request.getAttribute("destinationModelName"); %>
+    <input type="hidden" name="destinationModelName" value="${destinationModelName}"/>
+    <input type="hidden" name="csv2rdf" value="${csv2rdf}"/>
     
-   <input type="hidden" name="destinationModelName" value="<%=modelName%>"/>
+    <c:forEach var="sourceModelValue" items="${sourceModel}">
+        <input type="hidden" name="sourceModelName" value="${sourceModelValue}"/>
+    </c:forEach>
     
     <input class="submit" type="submit" value="Convert CSV"/>
     

webapp/web/jenaIngest/executeWorkflow.jsp

@@ -17,7 +17,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>

webapp/web/jenaIngest/generateTBox.jsp

@@ -17,7 +17,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>

webapp/web/jenaIngest/mergeResources.jsp

@@ -16,7 +16,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-	maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+	maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>
@@ -46,4 +46,4 @@
     <input type="checkbox" name="usePrimaryLabelOnly" value="Use Primary Label Only">Retain rdfs:labels only from Primary Resource</input>
 
     <p><input class="submit"type="submit" name="submit" value="Merge resources" /></p>
-</form>
+</form>

webapp/web/jenaIngest/permanentURI.jsp

@@ -16,7 +16,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-	maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+	maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>
@@ -63,4 +63,4 @@ Or <%String defaultNamespace = (String)request.getAttribute("defaultNamespace");
 </p>
 
 <p><input class="submit" type="submit" name="submit" value="Generate URIs" /></p>
-</form>
+</form>

webapp/web/jenaIngest/processStrings.jsp

@@ -17,7 +17,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>

webapp/web/jenaIngest/renameBNodes.jsp

@@ -17,7 +17,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>

webapp/web/jenaIngest/renameBNodesURISelect.jsp

@@ -12,6 +12,7 @@
 <%@ page import="java.util.HashMap" %>
 <%@ page import="java.util.Set" %>
 <%@ page import="java.util.Map.Entry" %>
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%>
 
 <%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
 <%@page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %>
@@ -22,12 +23,11 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>
 <script type="text/javascript" src="js/jquery.js"></script>
-<script type="text/javascript" src="js/jenaIngest/renameNode.js"></script>
 <script type="text/javascript">
 function selectProperties(){
 	document.getElementById("properties").disabled = false;
@@ -46,16 +46,24 @@ function disableProperties(){
 
     <h3>Select URI prefix</h3>
    
-	<p>URIs will be constructed from the following string:</p>
+    <c:if test="${!empty errorMsg}">
+       <p class="notice">${errorMsg}</p>
+    </c:if>
+   
+	<p>URIs will be constructed using the following base string:</p>
 	<input id="namespace" type="text" style="width:65%;" name="namespaceEtcStr"/> 
 
-    <p/>
+     <p/>
+
+<c:choose>
+  <c:when test="${enablePropertyPatternURIs}">    
+    <p>Each resource will be assigned a URI by taking the above string and 
+     adding either a random integer, or a string based on the value of one of the
+     the properties of the resource</p>
     
-    <p>You can concatenate above string with random integer OR your own pattern based on <b>values</b> of one of the properties (Properties will be enabled in the dropdown) </p>
-    
-    <input type="radio" value="integer" name="concatenate" checked="checked" onclick="disableProperties()"><b>No</b>, concatenate with random integer</input>
+    <input type="radio" value="integer" name="concatenate" checked="checked" onclick="disableProperties()">Use random integer</input>
     <br></br>
-    <input type="radio" value="pattern" name="concatenate" onclick="selectProperties()"><b>Yes</b>, concatenate with my pattern</input> 
+    <input type="radio" value="pattern" name="concatenate" onclick="selectProperties()">Use pattern based on values of </input> 
   
     
     <% Map<String,LinkedList<String>> propertyMap = (Map) request.getAttribute("propertyMap");
@@ -75,9 +83,21 @@ function disableProperties(){
     %>
     </select>
     <br></br>
-    <p>Enter your pattern that will prefix property value with an underscore eg. depID_$$$ where depID is your pattern and $$$ is the property value.</p>
+    <p>Enter a pattern using $$$ as the placeholder for the value of the property selected above.</p>
+    <p>For example, entering dept_$$$ might generate URIs with endings such as dept_Art or dept_Classics.</p>
     <input id="pattern" disabled="disabled" type="text" style="width:35%;" name="pattern"/> 
     
+  </c:when>
+  <c:otherwise>
+   <p>Each resource will be assigned a URI by taking the above string and 
+     adding a random integer.</p>
+   <input type="hidden" value="integer" name="concatenate"/>
+  </c:otherwise>
+</c:choose>
+    
+    <c:forEach var="sourceModelValue" items="${sourceModel}">
+        <input type="hidden" name="sourceModelName" value="${sourceModelValue}"/>
+    </c:forEach>
     
   
     <h3>Select Destination Model</h3>

webapp/web/jenaIngest/renameResource.jsp

@@ -13,7 +13,6 @@
 <vitro:confirmAuthorization />
 
 <script type="text/javascript" src="js/jquery.js"></script>
-<script type="text/javascript" src="js/jenaIngest/ingestUtils.js"></script>
 
 <h2><a class="ingestMenu" href="ingest">Ingest Menu</a> > Change Namespace of Resources</h2>
 
@@ -25,9 +24,13 @@ they will be updated to this format.</p>
 <p>This tool operates on the main web application model only, not on any 
    of the additional Jena models.</p>
 
+<c:if test="${!empty errorMsg}">
+    <p class="notice">${errorMsg}</p>
+</c:if>
+
 <form id="takeuri" action="ingest" method="get">
 <input type="hidden" name="action" value="renameResource"/>
-<p>Old namespace: <input id="uri1" type="text" size="52" name="uri1"/></p>
-<p>New namespace: <input id="uri2" type="text" size="52" name="uri2"/></p>
+<p>Old namespace: <input id="uri1" type="text" size="52" name="oldNamespace" value="${oldNamespace}" /></p>
+<p>New namespace: <input id="uri2" type="text" size="52" name="newNamespace" value="${newNamespace}" /></p>
 <p><input id="submit" type="submit" name="submit" value="Change namespace" /></p>
 </form>

webapp/web/jenaIngest/smushSingleModel.jsp

@@ -17,7 +17,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>

webapp/web/jenaIngest/sparqlConstruct.jsp

@@ -19,7 +19,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>
@@ -188,4 +188,4 @@ PREFIX <%=prefixText%>: <<%=urlText%>><%}}%>
 		<p><input type="checkbox" name="reasoning" value="pellet" />
 		include Pellet OWL-DL reasoning</p>
 	</c:otherwise>
-</c:choose> <input id="submit" type="submit" value="Execute CONSTRUCT" />
+</c:choose> <input id="submit" type="submit" value="Execute CONSTRUCT" />

webapp/web/jenaIngest/splitPropertyValues.jsp

@@ -17,7 +17,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>

webapp/web/jenaIngest/subtractModels.jsp

@@ -17,7 +17,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+        maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>

webapp/web/jenaIngest/xmlFileUpload.jsp

@@ -14,7 +14,7 @@
 
     ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
     if (maker == null) {
-		maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
+		maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
     }
 
 %>