diff --git a/example.deploy.properties b/example.deploy.properties
index 513b6236..40748b56 100644
--- a/example.deploy.properties
+++ b/example.deploy.properties
@@ -162,7 +162,7 @@ visualization.temporal = enabled
 # Absolute path on the server of the Harvester root directory.  
 # You must include the final slash.
 #
-harvester.location = /usr/local/vivo/harvester/
+# harvester.location = /usr/local/vivo/harvester/
 
 #
 # Default type(s) for Google Refine Reconciliation Service
diff --git a/productMods/css/harvester/fileharvest.css b/productMods/css/harvester/fileharvest.css
index 80a517ac..6d3dab78 100644
--- a/productMods/css/harvester/fileharvest.css
+++ b/productMods/css/harvester/fileharvest.css
@@ -32,4 +32,14 @@ a.help {
 }
 #harvestButton {
     margin-right: 10px;
+}
+#fileHarvestErrorHelp ol {
+    margin: 0 0 1.3em 2em;
+    list-style-type: decimal;
+    font-size: .9em;
+}
+#fileHarvestErrorHelp em {
+    font-family:"Courier New",Courier,mono;
+    font-style: normal;
+    color:#666;
 }
\ No newline at end of file
diff --git a/productMods/templates/freemarker/body/harvester/fileharvest.ftl b/productMods/templates/freemarker/body/harvester/fileharvest.ftl
index 0a5f7c0f..5952c790 100644
--- a/productMods/templates/freemarker/body/harvester/fileharvest.ftl
+++ b/productMods/templates/freemarker/body/harvester/fileharvest.ftl
@@ -1,5 +1,7 @@
 <#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
 
+<#-- <@dump var="harvesterLocation" /> -->
+
 <#if !(user.loggedIn && user.hasSiteAdminAccess)>
 
     <p>You must be an administrator to use this tool.</p>
@@ -13,224 +15,265 @@
         <p>The end user should not see this error under normal circumstances, so this is probably a bug and should be reported.</p>
         
     <#else>
-    
-        <script type="text/javascript">
-
-            var harvestProgressResponse;
-
-            function doHarvest()
-            {
-                document.getElementById("harvestButton").disabled = true;
-                document.getElementById("harvestButtonHelpText").innerHTML = "Please wait while your data is harvested.";
-
-                var request = createRequest();
-                request.onreadystatechange=function() {
-                    if(request.readyState == 4 && request.status == 200) {
-                        harvestProgressResponse = request.responseText;
-
-                        var json = eval("(" + harvestProgressResponse + ")");
-                        var scriptTextArea = document.getElementById("scriptTextArea");
-                        scriptTextArea.innerHTML = json.scriptText;
-
-                        window.setTimeout(continueHarvest, 1000);
-                    }
-                }
-                request.open("POST", "${postTo}", true);
-                request.setRequestHeader("content-type","application/x-www-form-urlencoded");
-                //request.send("${paramMode}=${modeHarvest}&${paramJob}=${job}");
-                request.send("${paramMode}=${modeHarvest}");
-            }
-
-
-            function continueHarvest()
-            {
-                var response = harvestProgressResponse;
-                var json = eval("(" + response + ")");
-
-                var logAppend = json.progressSinceLastCheck;
-                var progressTextArea = document.getElementById("progressTextArea");
-                progressTextArea.innerHTML = progressTextArea.innerHTML + logAppend;
-                progressTextArea.scrollTop = progressTextArea.scrollHeight;
-
-                if(!json.finished) {
+        
+        <h2><a class="ingestMenu" href="${urls.base}/ingest" title="Return to the Data Ingest Tools menu">Ingest Menu</a> > ${jobSpecificHeader}</h2>
+        
+        <#-- check to ensure harvester.location is set in deploy.properties -->
+        <#if harvesterLocation?has_content>
+            
+            <script type="text/javascript">
+                
+                var harvestProgressResponse;
+                
+                function doHarvest() {
+                    document.getElementById("harvestButton").disabled = true;
+                    document.getElementById("harvestButtonHelpText").innerHTML = "Please wait while your data is harvested.";
+                    
                     var request = createRequest();
                     request.onreadystatechange=function() {
                         if(request.readyState == 4 && request.status == 200) {
                             harvestProgressResponse = request.responseText;
+                            
+                            var json = eval("(" + harvestProgressResponse + ")");
+                            if(checkForFatalError(json))
+                                return;
+                            
+                            var scriptTextArea = document.getElementById("scriptTextArea");
+                            scriptTextArea.innerHTML = json.scriptText;
+                            
                             window.setTimeout(continueHarvest, 1000);
                         }
                     }
                     request.open("POST", "${postTo}", true);
-                    request.setRequestHeader("Content-type","application/x-www-form-urlencoded");
-                    //request.send("${paramMode}=${modeCheckStatus}&${paramJob}=${job}");
-                    request.send("${paramMode}=${modeCheckStatus}");
-                } else {
-
-                    // var linkHeader = document.getElementById("linkHeader");
-                    // linkHeader.style.display = "inline";
-                    $('#linkHeader').removeClass('hidden');
-
-                    var importedItems = document.getElementById("importedItems")
-
-                    if(json.newlyAddedUrls.length > 0) {
-                        for(var i = 0; i < json.newlyAddedUrls.length; i++) {
-
+                    request.setRequestHeader("content-type","application/x-www-form-urlencoded");
+                    //request.send("${paramMode}=${modeHarvest}&${paramJob}=${job}");
+                    request.send("${paramMode}=${modeHarvest}");
+                }
+                
+                function continueHarvest() {
+                    var response = harvestProgressResponse;
+                    var json = eval("(" + response + ")");
+                    if(checkForFatalError(json)) {
+                        return;
+                    }
+                    
+                    var logAppend = json.progressSinceLastCheck;
+                    var progressTextArea = document.getElementById("progressTextArea");
+                    progressTextArea.innerHTML = progressTextArea.innerHTML + logAppend;
+                    progressTextArea.scrollTop = progressTextArea.scrollHeight;
+                    
+                    if(!json.finished) {
+                        var request = createRequest();
+                        request.onreadystatechange=function() {
+                            if(request.readyState == 4 && request.status == 200) {
+                                harvestProgressResponse = request.responseText;
+                                window.setTimeout(continueHarvest, 1000);
+                            }
+                        }
+                        request.open("POST", "${postTo}", true);
+                        request.setRequestHeader("Content-type","application/x-www-form-urlencoded");
+                        //request.send("${paramMode}=${modeCheckStatus}&${paramJob}=${job}");
+                        request.send("${paramMode}=${modeCheckStatus}");
+                    } else {
+                        // var linkHeader = document.getElementById("linkHeader");
+                        // linkHeader.style.display = "inline";
+                        $('#linkHeader').removeClass('hidden');
+                        
+                        var importedItems = document.getElementById("importedItems")
+                        
+                        if(json.newlyAddedUrls.length > 0) {
+                            for(var i = 0; i < json.newlyAddedUrls.length; i++) {
+                                
+                                var newLi = document.createElement("li");
+                                newLi.innerHTML = "<a href=\"" + json.newlyAddedUrls[i] + "\" target=\"_blank\">" + json.newlyAddedUris[i] + "</a>";
+                                importedItems.appendChild(newLi);
+                            }
+                        } else {
                             var newLi = document.createElement("li");
-                            newLi.innerHTML = "<a href=\"" + json.newlyAddedUrls[i] + "\" target=\"_blank\">" + json.newlyAddedUris[i] + "</a>";
+                            newLi.innerHTML = "${jobSpecificNoNewDataMessage}";
                             importedItems.appendChild(newLi);
                         }
-                    } else {
-
-                        var newLi = document.createElement("li");
-                        newLi.innerHTML = "${jobSpecificNoNewDataMessage}";
-                        importedItems.appendChild(newLi);
+                        
+                        document.getElementById("harvestButtonHelpText").innerHTML = "Harvest complete.  For another, please refresh the page.";
                     }
-
-                    document.getElementById("harvestButtonHelpText").innerHTML = "Harvest complete.  For another, please refresh the page.";
                 }
-            }
-
-
-
-            function createRequest() {
-                var request;
-                if (window.XMLHttpRequest) {
-                    request = new XMLHttpRequest();
-                } else {
-                    request = new ActiveXObject("Microsoft.XMLHTTP");
+                
+                function createRequest() {
+                    var request;
+                    if (window.XMLHttpRequest) {
+                        request = new XMLHttpRequest();
+                    } else {
+                        request = new ActiveXObject("Microsoft.XMLHTTP");
+                    }
+                    return request;
                 }
-                return request;
-            }   
-
-            function fileResponse()
-            {
-                var response = frames["uploadTarget"].document.getElementsByTagName("body")[0].innerHTML;
-                var json = eval("(" + response + ")");
-
-                var fileListing = document.getElementById("fileListing")
-                var newLi = document.createElement("li");
-
-                if(json.success)
-                    newLi.innerHTML = json.fileName + " <span style=\"color:green\">" + json.errorMessage + "</span>";
-                else
-                    newLi.innerHTML = json.fileName + " <span style=\"color:red\">upload failed: " + json.errorMessage + "</span>";
-                fileListing.appendChild(newLi);
-
-                document.getElementById("${paramFirstUpload}").value = "false";
-
-                //document.getElementById("responseArea").innerHTML = response;
-            }
-
-            function init()
-            {
-                document.getElementById("harvestButton").disabled = false;
-
-                document.getElementById("${paramFirstUpload}").value = "true";
-                document.getElementById("fileUploadForm").onsubmit = function()
-                {
-                    document.getElementById("fileUploadForm").target = "uploadTarget";
-                    document.getElementById("uploadTarget").onload = fileResponse;
+                
+                function fileResponse() {
+                    var response = frames["uploadTarget"].document.getElementsByTagName("body")[0].innerHTML;
+                    var json = eval("(" + response + ")");
+                    if(checkForFatalError(json)) {
+                        return;
+                    }
+                    
+                    var fileListing = document.getElementById("fileListing")
+                    var newLi = document.createElement("li");
+                    
+                    if (json.success) {
+                        newLi.innerHTML = json.fileName + " <span style=\"color:green\">" + json.errorMessage + "</span>";
+                    } else {
+                        newLi.innerHTML = json.fileName + " <span style=\"color:red\">upload failed: " + json.errorMessage + "</span>";
+                    }
+                    
+                    fileListing.appendChild(newLi);
+                    
+                    document.getElementById("${paramFirstUpload}").value = "false";
+                    
+                    //document.getElementById("responseArea").innerHTML = response;
                 }
-                document.getElementById("downloadTemplateForm").onsubmit = function()
-                {
-                    document.getElementById("downloadTemplateForm").target = "uploadTarget";
+                
+                function init() {
+                        document.getElementById("harvestButton").disabled = false;
+                        
+                        document.getElementById("${paramFirstUpload}").value = "true";
+                        document.getElementById("fileUploadForm").onsubmit = function()
+                        {
+                            document.getElementById("fileUploadForm").target = "uploadTarget";
+                            document.getElementById("uploadTarget").onload = fileResponse;
+                        }
+                        document.getElementById("downloadTemplateForm").onsubmit = function()
+                        {
+                            document.getElementById("downloadTemplateForm").target = "uploadTarget";
+                        }
                 }
-            }
-            
-            window.onload = init;
-            
-            $(document).ready(function() {
-                $('a.help').click(function() {
-                    $('#csvHelp-collapsible').toggleClass('hidden');
-                    return false;
+                
+                function checkForFatalError(json) {
+                    if(json.fatalError) {
+                        handleFatalError();
+                        return true;
+                    } else {
+                        return false;
+                    }
+                }
+                
+                function handleFatalError() {
+                    $('#fileHarvestErrorHelp').removeClass('hidden');
+                    $('#fileHarvestForm').addClass('hidden');
+                } 
+                
+                window.onload = init;
+                
+                $(document).ready(function() {
+                    $('a.help').click(function() {
+                        $('#csvHelp-collapsible').toggleClass('hidden');
+                        return false;
+                    });
+                    
+                    $('#harvestButton').click(function() {
+                        doHarvest();
+                        return false;
+                    });
                 });
                 
-                $('#harvestButton').click(function() {
-                    doHarvest();
-                    return false;
-                });
-            });
-
-        </script>
-        
-        <h2><a class="ingestMenu" href="${urls.base}/ingest">Ingest Menu</a> > ${jobSpecificHeader}</h2>
-        
-        <div id="step1" class="testfile-step">
-            <h3 class="testfile-step-header">Step 1</h3>
-            <div id="step1-inner" class="testfile-step-body">
-                <h4 class="testfile-step-subheader">Download template</h4>
-                <form id="downloadTemplateForm" method="post" action=${postTo}>
-                    <input type="hidden" id="${paramMode}" name="${paramMode}" value="${modeDownloadTemplate}" />
-                    <p><input id="submit" type="submit" name="submit" value="Download" /> ${jobSpecificDownloadHelp}</p>
-                </form>
+            </script>
+            
+            <div id="fileHarvestErrorHelp" class="hidden">
+                <p>An error has occurred and the file harvest cannot continue.</p>
+                
+                <p>This is most likely due to an improper Harvester configuration. Please ensure the following:</p>
+                
+                <ol>
+                    <li>VIVO Harvester is installed.</li>
+                    <li>The <em>harvester.location</em> property in deploy.properties is pointed to the Harvester installation directory.</li>
+                    <li>In VIVO Harvester, the web server user (typically tomcat6) has read and write access to the <em>vivo/</em> directory and all of its children.</li>
+                    <li>In VIVO Harvester, the <em>logs/</em> directory exists and the web server user has read and write access to it.</li>
+                    <li>In VIVO Harvester, the file <em>vivo/config/vivo.xml</em> is properly configured with your database information and namespace.</li>
+                </ol>
             </div>
-            <div class="clearBothDiv" />
-        </div>
-        
-        <div id="step2" class="testfile-step">
-            <h3 class="testfile-step-header">Step 2</h3>
-            <div id="step2-inner" class="testfile-step-body">
-                <h4 class="testfile-step-subheader">Fill in data <a class="help" href="#">Help</a></h4>
-                <div id="csvHelp-collapsible" class="hidden">
-                    <div id="csvHelp-indented">
-                        ${jobSpecificFillInHelp}
+            
+            <div id="fileHarvestForm">
+                <div id="step1" class="testfile-step">
+                    <h3 class="testfile-step-header">Step 1</h3>
+                    <div id="step1-inner" class="testfile-step-body">
+                        <h4 class="testfile-step-subheader">Download template</h4>
+                        <form id="downloadTemplateForm" method="post" action=${postTo}>
+                            <input type="hidden" id="${paramMode}" name="${paramMode}" value="${modeDownloadTemplate}" />
+                            <p><input id="submit" type="submit" name="submit" value="Download" /> ${jobSpecificDownloadHelp}</p>
+                        </form>
                     </div>
                 </div>
-                <p>Fill in the template with your data.  You may fill in multiple templates if you wish to harvest multiple files at once.</p>
-                <div id="csvHelp">
+                
+                <div id="step2" class="testfile-step">
+                    <h3 class="testfile-step-header">Step 2</h3>
+                    <div id="step2-inner" class="testfile-step-body">
+                        <h4 class="testfile-step-subheader">Fill in data <a class="help" href="#">Help</a></h4>
+                        <div id="csvHelp-collapsible" class="hidden">
+                            <div id="csvHelp-indented">
+                                ${jobSpecificFillInHelp}
+                            </div>
+                        </div>
+                        <p>Fill in the template with your data.  You may fill in multiple templates if you wish to harvest multiple files at once.</p>
+                        <div id="csvHelp">
+                        </div>
+                    </div>
+                </div>
+                
+                <div id="step3" class="testfile-step">
+                    <h3 class="testfile-step-header">Step 3</h3>
+                    <div id="step3-inner" class="testfile-step-body">
+                        <h4 class="testfile-step-subheader">Upload file(s)</h4>
+                        <p>Upload your filled-in template(s).</p>
+                        <form id="fileUploadForm" method="post" enctype="multipart/form-data" action=${postTo}>
+                            <input type="hidden" id="${paramFirstUpload}" name="${paramFirstUpload}" value="true" />
+                            <!--<input type="hidden" id="${paramJob}" name="${paramJob}" value="${job}" /> -->
+                            <input type="file" name="${paramUploadedFile}" />
+                            <input type="submit" name="submit" value="Upload" />
+                            <iframe id="uploadTarget" name="uploadTarget" src=""></iframe>
+                        </form>
+                        <h5>Uploaded files</h5>
+                        <ul id="fileListing">
+                        </ul>
+                    </div>
+                </div>
+                
+                <div id="step4" class="testfile-step">
+                    <h3 class="testfile-step-header">Step 4</h3>
+                    <div id="step4-inner" class="testfile-step-body">
+                        <h4 class="testfile-step-subheader">Harvest</h4>
+                        <p><input type="button" name="harvestButton" id="harvestButton" class="green button" value="Harvest" /><span id="harvestButtonHelpText">Click the button to harvest your file(s).</span></p>
+                    </div>
+                </div>
+                
+                <div id="step5" class="testfile-step">
+                    <h3 class="testfile-step-header">Step 5</h3>
+                    <div id="step5-inner" class="testfile-step-body">
+                        <h4 class="testfile-step-subheader">View results</h4>
+                        <div id="script">
+                            <h5>Script being executed</h5>
+                            <textarea cols="100" rows="20" readonly="readonly" id="scriptTextArea"></textarea>      
+                        </div>
+                        <div id="progress">
+                            <h5>Progress</h5>
+                            <textarea cols="100" rows="20" readonly="readonly" id="progressTextArea"></textarea>        
+                        </div>
+                        <div id="summary">
+                            <h5 id="linkHeader" class="hidden">${jobSpecificLinkHeader}</h5>
+                            <ul id="importedItems">
+                            </ul>
+                        </div>
+                    </div>
                 </div>
             </div>
-            <div class="clearBothDiv" />
-        </div>
-        
-        <div id="step3" class="testfile-step">
-            <h3 class="testfile-step-header">Step 3</h3>
-            <div id="step3-inner" class="testfile-step-body">
-                <h4 class="testfile-step-subheader">Upload file(s)</h4>
-                <p>Upload your filled-in template(s).</p>
-                <form id="fileUploadForm" method="post" enctype="multipart/form-data" action=${postTo}>
-                    <input type="hidden" id="${paramFirstUpload}" name="${paramFirstUpload}" value="true" />
-                    <!--<input type="hidden" id="${paramJob}" name="${paramJob}" value="${job}" /> -->
-                    <input type="file" name="${paramUploadedFile}" />
-                    <input type="submit" name="submit" value="Upload" />
-                    <iframe id="uploadTarget" name="uploadTarget" src=""></iframe>
-                </form>
-                <h5>Uploaded files</h5>
-                <ul id="fileListing">
-                </ul>
+            
+        <#else>
+            
+            <div id="fileHarvestErrorHelp">
+                <p>The <em>harvester.location</em> property in deploy.properties is undefined.</p>
+                
+                <p>In order to use this feature, please define a value for this property that points to the Harvester installation directory before redeploying and restarting the application.</p>
             </div>
-            <div class="clearBothDiv" />
-        </div>
-        
-        <div id="step4" class="testfile-step">
-            <h3 class="testfile-step-header">Step 4</h3>
-            <div id="step4-inner" class="testfile-step-body">
-                <h4 class="testfile-step-subheader">Harvest</h4>
-                <p><input type="button" name="harvestButton" id="harvestButton" class="green button" value="Harvest" /><span id="harvestButtonHelpText">Click the button to harvest your file(s).</span></p>
-            </div>
-            <div class="clearBothDiv" />
-        </div>
-        
-        <div id="step5" class="testfile-step">
-            <h3 class="testfile-step-header">Step 5</h3>
-            <div id="step5-inner" class="testfile-step-body">
-                <h4 class="testfile-step-subheader">View results</h4>
-                <div id="script">
-                    <h5>Script being executed</h5>
-                    <textarea cols="100" rows="20" readonly="readonly" id="scriptTextArea"></textarea>      
-                </div>
-                <div id="progress">
-                    <h5>Progress</h5>
-                    <textarea cols="100" rows="20" readonly="readonly" id="progressTextArea"></textarea>        
-                </div>
-                <div id="summary">
-                    <h5 id="linkHeader" class="hidden">${jobSpecificLinkHeader}</h5>
-                    <ul id="importedItems">
-                    </ul>
-                </div>
-            </div>
-            <div class="clearBothDiv" />
-        </div>
+            
+        <#-- if harvester.location is defined -->
+        </#if>
         
         ${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/harvester/fileharvest.css" />')}
         
diff --git a/src/edu/cornell/mannlib/vitro/webapp/controller/harvester/FileHarvestController.java b/src/edu/cornell/mannlib/vitro/webapp/controller/harvester/FileHarvestController.java
index 693bb26d..678b6200 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/controller/harvester/FileHarvestController.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/controller/harvester/FileHarvestController.java
@@ -52,6 +52,8 @@ public class FileHarvestController extends FreemarkerHttpServlet {
     private static final Log log = LogFactory.getLog(FileHarvestController.class);
     private static final String TEMPLATE_DEFAULT = "fileharvest.ftl";
 
+    private static final String NORMAL_TERMINATION_LAST_OUTPUT = "File Harvest completed successfully";
+    
     private static final String PARAMETER_FIRST_UPLOAD = "firstUpload";
     private static final String PARAMETER_UPLOADED_FILE = "uploadedFile";
     private static final String PARAMETER_MODE = "mode";
@@ -140,6 +142,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
             FileHarvestJob jobObject = getJob(vreq, job);
 
             Map<String, Object> body = new HashMap<String, Object>();
+            String harvesterPath = getHarvesterPath(vreq);
             //body.put("uploadPostback", "false");
             body.put("paramFirstUpload", PARAMETER_FIRST_UPLOAD);
             body.put("paramUploadedFile", PARAMETER_UPLOADED_FILE);
@@ -150,6 +153,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
             body.put("modeDownloadTemplate", MODE_DOWNLOAD_TEMPLATE);
             body.put("job", job);
             body.put("jobKnown", jobKnown);
+            body.put("harvesterLocation", harvesterPath);
             body.put("postTo", POST_TO + "?" + PARAMETER_JOB + "=" + job);
             body.put("jobSpecificHeader", (jobObject != null) ? jobObject.getPageHeader() : "");
             body.put("jobSpecificLinkHeader", (jobObject != null) ? jobObject.getLinkHeader() : "");
@@ -284,7 +288,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
     private void doFileUploadPost(HttpServletRequest request, HttpServletResponse response)
         throws IOException, ServletException {
 
-        JSONObject json = new JSONObject();
+        JSONObject json = generateJson(false);
         try {
             VitroRequest vreq = new VitroRequest(request);
 
@@ -392,7 +396,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
             }
         } catch(Exception e) {
             log.error(e, e);
-            return;
+            json = generateJson(true);
         }
 
         //write the prepared response
@@ -407,6 +411,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
      */
     private void doHarvestPost(HttpServletRequest request, HttpServletResponse response) {
 
+    	JSONObject json;
         try {
             VitroRequest vreq = new VitroRequest(request);
             FileHarvestJob job = getJob(vreq, vreq.getParameter(PARAMETER_JOB));
@@ -416,18 +421,23 @@ public class FileHarvestController extends FreemarkerHttpServlet {
             String script = job.getScript();
             String additionsFilePath = job.getAdditionsFilePath();
             String scriptFileLocation = getScriptFileLocation(vreq);
-            runScript(getSessionId(request), script, additionsFilePath, scriptFileLocation);
+            runScript(getSessionId(request), script, additionsFilePath, scriptFileLocation, job);
 
-            JSONObject json = new JSONObject();
+            json = generateJson(false);
             json.put("progressSinceLastCheck", "");
             json.put("scriptText", script);
             json.put("finished", false);
 
-            response.getWriter().write(json.toString());
-
         } catch(Exception e) {
+        	json = generateJson(true);
             log.error(e, e);
         }
+        
+        try {
+        	response.getWriter().write(json.toString());
+        } catch(IOException e) {
+        	log.error(e, e);
+        }
     }
 
     /**
@@ -439,6 +449,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
      */
     private void doCheckHarvestStatusPost(HttpServletRequest request, HttpServletResponse response) {
 
+        JSONObject json;
         try {
             String newline = "\n";
 
@@ -463,6 +474,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
                 }
 
                 boolean finished = sessionInfo.isFinished();
+                boolean abnormalTermination = false;
 
                 VitroRequest vreq = new VitroRequest(request);
                 ArrayList<String> newlyAddedUrls = new ArrayList<String>();
@@ -478,21 +490,35 @@ public class FileHarvestController extends FreemarkerHttpServlet {
 
                     //remove all entries in "sessionIdTo..." mappings for this session ID
                     clearSessionInfo(sessionId);
+                    
+                    if(sessionInfo.getAbnormalTermination()) 
+                    	abnormalTermination = true;
                 }
 
-                JSONObject json = new JSONObject();
-                json.put("progressSinceLastCheck", progressSinceLastCheck);
-                json.put("finished", finished);
-                json.put("newlyAddedUris", newlyAddedUris);
-                json.put("newlyAddedUrls", newlyAddedUrls);
-
-                response.getWriter().write(json.toString());
+                if(!abnormalTermination) {
+	                json = generateJson(false);
+	                json.put("progressSinceLastCheck", progressSinceLastCheck);
+	                json.put("finished", finished);
+	                json.put("newlyAddedUris", newlyAddedUris);
+	                json.put("newlyAddedUrls", newlyAddedUrls);
+                } else {
+                	json = generateJson(true);
+                	log.error("File harvest terminated abnormally.");
+                }
             } else { //if we have not started a harvest thread, the browser should not have made this request to begin with.  Bad browser, very bad browser.
+            	json = generateJson(true);
                 log.error("Attempt to check status of a harvest that was never started!  (Session ID " + sessionId + ")");
             }
         } catch(Exception e) {
+        	json = generateJson(true);
             log.error(e, e);
         }
+        
+        try {
+        	response.getWriter().write(json.toString());
+        } catch(IOException e) {
+        	log.error(e, e);
+        }
     }
 
     private void doDownloadTemplatePost(HttpServletRequest request, HttpServletResponse response) {
@@ -549,10 +575,10 @@ public class FileHarvestController extends FreemarkerHttpServlet {
     }
 
 
-    private void runScript(String sessionId, String script, String additionsFilePath, String scriptFileLocation) {
+    private void runScript(String sessionId, String script, String additionsFilePath, String scriptFileLocation, FileHarvestJob job) {
         clearSessionInfo(sessionId);
 
-        ScriptRunner runner = new ScriptRunner(sessionId, script, additionsFilePath, scriptFileLocation);
+        ScriptRunner runner = new ScriptRunner(sessionId, script, additionsFilePath, scriptFileLocation, job);
         SessionInfo info = new SessionInfo(sessionId, runner);
         sessionIdToSessionInfo.put(sessionId, info);
         runner.start();
@@ -604,7 +630,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
      * @param additionsFile the file containing the newly-added RDF/XML
      * @param newlyAddedUris a list in which to place the newly added URIs
      */
-    private void extractNewlyAddedUris(File additionsFile, List<String> newlyAddedUris) {
+    private void extractNewlyAddedUris(File additionsFile, List<String> newlyAddedUris, FileHarvestJob job) {
 
         try {
             DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -618,7 +644,16 @@ public class FileHarvestController extends FreemarkerHttpServlet {
                 Node node = descriptionNodes.item(i);
 
                 ArrayList<String> types = getRdfTypes(node);
-                if(types.contains("http://vivoweb.org/ontology/core#Grant")) { //todo: generalize
+                
+                boolean match = false;
+                String[] validRdfTypesForJob = job.getRdfTypesForLinks();
+                for(String rdfType : validRdfTypesForJob) {
+                	if(types.contains(rdfType))
+                		match = true;
+                	break;
+                }
+                
+                if(match) {
 
                     NamedNodeMap attributes = node.getAttributes();
                     Node aboutAttribute = attributes.getNamedItemNS("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "about");
@@ -705,6 +740,21 @@ public class FileHarvestController extends FreemarkerHttpServlet {
     }
 
 
+    /**
+     * Create a new JSON object
+     * @param fatalError whether the fatal error flag should be set on this object
+     * @return the new JSON object
+     */
+    private JSONObject generateJson(boolean fatalError) {
+    	JSONObject json = null;
+    	try {
+	        json = new JSONObject();
+	        json.put("fatalError", fatalError);
+    	} catch(JSONException e) {
+    		log.error(e.getMessage(), e);
+    	}
+        return json;
+    }
 
 
 
@@ -743,6 +793,11 @@ public class FileHarvestController extends FreemarkerHttpServlet {
          */
         private boolean finished = false;
 
+        /**
+         * Flag indicating that the thread finished abnormally.
+         */
+        private boolean abnormalTermination = false;
+
 
         /**
          * Newly added entries to VIVO, for this user session.
@@ -757,6 +812,13 @@ public class FileHarvestController extends FreemarkerHttpServlet {
             this.harvestThread = harvestThread;
         }
 
+        public void setAbnormalTermination() {
+        	abnormalTermination = true;
+        }
+        public boolean getAbnormalTermination() {
+        	return abnormalTermination;
+        }
+        
         public void finish() {
             finished = true;
         }
@@ -786,14 +848,16 @@ public class FileHarvestController extends FreemarkerHttpServlet {
         private final String script;
         private final String additionsFilePath;
         private final String scriptFileLocation;
+        private final FileHarvestJob job;
 
         private volatile boolean abort = false;
 
-        public ScriptRunner(String sessionId, String script, String additionsFilePath, String scriptFileLocation) {
+        public ScriptRunner(String sessionId, String script, String additionsFilePath, String scriptFileLocation, FileHarvestJob job) {
             this.sessionId = sessionId;
             this.script = script;
             this.additionsFilePath = additionsFilePath;
             this.scriptFileLocation = scriptFileLocation; 
+            this.job = job;
         }
 
         public void abortRun() {
@@ -804,6 +868,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
         @Override
         public void run() {
             SessionInfo sessionInfo = sessionIdToSessionInfo.get(sessionId);
+            boolean normalTerminationLineFound = false;
             if(sessionInfo != null) {
                 try {
                     ArrayList<String> unsentLogLines = sessionInfo.unsentLogLines;
@@ -820,6 +885,8 @@ public class FileHarvestController extends FreemarkerHttpServlet {
                     BufferedReader processOutputReader = new BufferedReader(new InputStreamReader(pr.getInputStream()));
                     for(String line = processOutputReader.readLine(); line != null; line = processOutputReader.readLine()) {
 
+                    	normalTerminationLineFound = line.endsWith(NORMAL_TERMINATION_LAST_OUTPUT); //set every read to ensure it's the last line
+                    	
                         //don't add stuff to this list if the main thread is running a "transaction" of copying out the data to send to client and then clearing the list
                         synchronized(unsentLogLines) {
                             unsentLogLines.add(line);
@@ -857,7 +924,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
 
                         File additionsFile = new File(this.additionsFilePath);
                         if(additionsFile.exists())
-                            extractNewlyAddedUris(additionsFile, sessionInfo.newlyAddedUris);
+                            extractNewlyAddedUris(additionsFile, sessionInfo.newlyAddedUris, this.job);
                         else
                             log.error("Additions file not found: " + this.additionsFilePath);
                     }
@@ -867,10 +934,10 @@ public class FileHarvestController extends FreemarkerHttpServlet {
                     log.error(e, e);
                 } finally {
                     sessionInfo.finish();
+                    if(!normalTerminationLineFound)
+                    	sessionInfo.setAbnormalTermination();
                 }
             }
         }
     }
-}
-
-
+}
\ No newline at end of file