From 10fcc55c46753f1c1f3e2b5a2659263d7b64578e Mon Sep 17 00:00:00 2001
From: Rogan Creswick <creswick@gmail.com>
Date: Sun, 16 Jun 2013 22:08:45 -0700
Subject: removed debugging statements from upGoerFive rule, caught some
 exceptions in HeadlessAtom

---
 .../language-processing/natural/upGoerFive.js      | 39 ++++++++++------------
 .../main/java/com/galois/fiveui/HeadlessAtom.java  | 14 ++++++--
 .../src/main/java/com/galois/fiveui/Reporter.java  |  2 +-
 3 files changed, 30 insertions(+), 25 deletions(-)

diff --git a/exampleData/ruleSets/language-processing/natural/upGoerFive.js b/exampleData/ruleSets/language-processing/natural/upGoerFive.js
index fb17a54..092a181 100644
--- a/exampleData/ruleSets/language-processing/natural/upGoerFive.js
+++ b/exampleData/ruleSets/language-processing/natural/upGoerFive.js
@@ -1,6 +1,6 @@
 var natural = require('natural');
 
-rule =  {};
+rule = {};
 rule.name = "Common words";
 rule.description = "Identifies rare word use (words not in the 1000 most common English word list).";
 
@@ -144,25 +144,25 @@ var stemmer = natural.PorterStemmer;
 var tokenizer = new natural.TreebankWordTokenizer();
 
 var getTextNodesIn = function (node, includeWhitespaceNodes) {
-    var textNodes = [], whitespace = /^\s*$/;
+  var textNodes = [], whitespace = /^\s*$/;
 
-    function getTextNodes(node) {
-        if ($(node).attr('id') == 'fiveui-top') {
-          return;
-        }
-        if (node.nodeType == 3) {
-            if (includeWhitespaceNodes || !whitespace.test(node.nodeValue)) {
-                textNodes.push(node);
-            }
-        } else {
-            for (var i = 0, len = node.childNodes.length; i < len; ++i) {
-                getTextNodes(node.childNodes[i]);
-            }
-        }
+  function getTextNodes(node) {
+    if ($(node).attr('id') == 'fiveui-top') {
+      return;
     }
+    if (node.nodeType == 3) {
+      if (includeWhitespaceNodes || !whitespace.test(node.nodeValue)) {
+        textNodes.push(node);
+      }
+    } else {
+      for (var i = 0, len = node.childNodes.length; i < len; ++i) {
+        getTextNodes(node.childNodes[i]);
+      }
+    }
+  }
 
-    getTextNodes(node);
-    return textNodes;
+  getTextNodes(node);
+  return textNodes;
 };
 
 var isCommonWord = function(word) {
@@ -173,11 +173,9 @@ var isPunctuation = function(str) {
   return _.contains(['&', '%', '(', ')', ';', ':', '.', ',', '"', "'", '`', '!', '?' ], str);
 };
 
-
 var markWords = function(obj, report) {
   var toks = tokenizer.tokenize($(obj).text());
   var rawObj = $('<p></p>', {id: 'text'});
-//  $(obj).empty();
   $(obj).replaceWith(rawObj);
 
   _.each(toks, function(tok) {
@@ -192,14 +190,11 @@ var markWords = function(obj, report) {
 };
 
 rule.rule = function(report) {
-  console.log("checking for rare words");
   fiveui.query('body').each(
     function(i){
       var nodes = getTextNodesIn(this);
       _.map(nodes, function(n){
-              console.log(n);
               markWords(n, report);
             });
     });
-  console.log("done checking for rare words");
 };
\ No newline at end of file
diff --git a/src/batchtools/headless/src/main/java/com/galois/fiveui/HeadlessAtom.java b/src/batchtools/headless/src/main/java/com/galois/fiveui/HeadlessAtom.java
index 01ffae0..12da948 100644
--- a/src/batchtools/headless/src/main/java/com/galois/fiveui/HeadlessAtom.java
+++ b/src/batchtools/headless/src/main/java/com/galois/fiveui/HeadlessAtom.java
@@ -48,8 +48,18 @@ public class HeadlessAtom {
      * @throws JsonParseException
      */
     public static HeadlessAtom fromJsonObject(JsonObject obj, String dir) throws IOException {
-		String url = obj.get("url").getAsString();
-		String ruleSet = obj.get("ruleSet").getAsString();
+		String url = null;
+		String ruleSet = null;
+		
+		try {
+			url = obj.get("url").getAsString();
+		} catch (NullPointerException e) {
+		}
+
+		try {
+			ruleSet = obj.get("ruleSet").getAsString();
+		} catch (NullPointerException e) {
+		}	
 
 		if (url == null || ruleSet == null) {
 			throw new JsonParseException("could get either 'url' or 'ruleSet' properties");
diff --git a/src/batchtools/headless/src/main/java/com/galois/fiveui/Reporter.java b/src/batchtools/headless/src/main/java/com/galois/fiveui/Reporter.java
index 5c0b233..cad8bee 100644
--- a/src/batchtools/headless/src/main/java/com/galois/fiveui/Reporter.java
+++ b/src/batchtools/headless/src/main/java/com/galois/fiveui/Reporter.java
@@ -92,7 +92,7 @@ public class Reporter {
 			h1().text("Headless Run Summary").end();
 			p();
 				ul();
-				li().a().href("byUrl.html").text("Results organized by URL").end().end();
+				li().a().href("byURL.html").text("Results organized by URL").end().end();
 				li().a().href("byRule.html").text("Results organized by Rule").end().end();
 				end();
 			end();
-- 
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