From aaf6587a1a5945802ab8fd471798c9ab20193340 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Thu, 7 Apr 2016 23:20:11 -0500
Subject: [PATCH 01/21] Modified timed checking for existing components to
 allow for ignorable timed components

---
 runestone/assess/js/timed.js                 | 78 ++++++++++----------
 runestone/assess/js/timedfitb.js             |  9 ++-
 runestone/assess/js/timedmc.js               | 18 ++++-
 runestone/clickableArea/js/timedclickable.js |  9 ++-
 runestone/dragndrop/js/timeddnd.js           | 10 ++-
 5 files changed, 80 insertions(+), 44 deletions(-)

diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index 12148f2f7..62245f2f8 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -90,10 +90,10 @@ Timed.prototype.renderTimedAssess = function () {
     this.renderNavControls();
     this.renderSubmitButton();
     this.renderFeedbackContainer();
-	
+
     // Replace intermediate HTML with rendered HTML
     $(this.origElem).replaceWith(this.assessDiv);
-    
+
     // check if already taken and if so show results
     this.tookTimedExam();
     if (this.taken) {
@@ -177,7 +177,7 @@ Timed.prototype.renderNavControls = function () {
 	this.navDiv.appendChild(this.pagNavList);
     this.break = document.createElement("br");
     this.navDiv.appendChild(this.break);
-    
+
     // render the question number jump buttons
     this.qNumList = document.createElement("ul");
 	$(this.qNumList).attr("id", "pageNums");
@@ -191,18 +191,18 @@ Timed.prototype.renderNavControls = function () {
             $(tmpLi).addClass("active");
         }
         tmpLi.appendChild(tmpA);
-        this.qNumList.appendChild(tmpLi);	
+        this.qNumList.appendChild(tmpLi);
     }
     this.navDiv.appendChild(this.qNumList);
-	this.navBtnListeners();  
-	
+	this.navBtnListeners();
+
 	$(function(){
 		var tenSet = $("ul#pageNums li");
 		for (var i = 0; i < tenSet.length; i += 10) {
 			tenSet.slice(i, i + 10).wrapAll("<ul class=\"pagination\"></ul>");
 		}
 	});
-	
+
 };
 
 Timed.prototype.navBtnListeners = function() {
@@ -210,18 +210,18 @@ Timed.prototype.navBtnListeners = function() {
 	this.pagNavList.addEventListener("click", function (event) {
 		if ($("div#timed_Test form input[name='group1']").is(":checked")) {
 			$("ul#pageNums > ul > li:eq(" + this.currentQuestionIndex +")").addClass("answered");
-		}	
+		}
 		var target = $(event.target).text();
 		if (target.match(/Next/)) {
 			if ($(this.rightContainer).hasClass("disabled")) {
-				return; 
-			} 
+				return;
+			}
 			this.currentQuestionIndex++;
-		} 
+		}
 		else if (target.match(/Prev/)) {
 			if ($(this.leftContainer).hasClass("disabled")) {
 				return;
-			} 
+			}
 			this.currentQuestionIndex--;
 		}
 		this.renderTimedQuestion();
@@ -241,7 +241,7 @@ Timed.prototype.navBtnListeners = function() {
 		}
 		for (var i = 0; i < this.qNumList.childNodes.length; i++) {
 			for (var j = 0; j < this.qNumList.childNodes[i].childNodes.length; j++) {
-				$(this.qNumList.childNodes[i].childNodes[j]).removeClass("active"); 
+				$(this.qNumList.childNodes[i].childNodes[j]).removeClass("active");
 			}
 		}
 		var target = $(event.target).text();
@@ -250,7 +250,7 @@ Timed.prototype.navBtnListeners = function() {
 		this.renderTimedQuestion();
 		this.ensureButtonSafety();
 	}.bind(this), false);
-	
+
 };
 
 Timed.prototype.renderSubmitButton = function () {
@@ -538,19 +538,21 @@ Timed.prototype.checkScore = function () {
     this.skippedStr = "";
     this.incorrectStr = "";
     // Gets the score of each problem
+
     for (var i = 0; i < this.renderedQuestionArray.length; i++) {
         var correct = this.renderedQuestionArray[i].checkCorrectTimed();
-        if (correct) {
-		    this.score++;
-			this.correctStr = this.correctStr + (i + 1) + ", ";				
-			
+        if (correct == "T") {
+            this.score++;
+            this.correctStr = this.correctStr + (i + 1) + ", ";
+
+        } else if (correct == "F") {
+            this.incorrect++;
+            this.incorrectStr = this.incorrectStr + (i + 1) + ", ";
         } else if (correct === null) {
             this.skipped++;
-			this.skippedStr = this.skippedStr + (i + 1) + ", ";
-			
+            this.skippedStr = this.skippedStr + (i + 1) + ", ";
         } else {
-            this.incorrect++;
-			this.incorrectStr = this.incorrectStr + (i + 1) + ", ";
+            // ignored question; just do nothing
         }
     }
 	// remove extra comma and space at end if any
@@ -610,27 +612,27 @@ Timed.prototype.restoreFromStorage = function () {
 };
 
 Timed.prototype.displayScore = function () {
- 
+
 	if (this.showResults)
-    {   
-       // If we have the list of 
+    {
+       // If we have the list of
        if (this.correctStr.length > 0 || this.incorrectStr.length > 0 || this.skippedStr.length > 0)
        {
           var scoreString = "Num Correct: " + this.score + ". Questions: " + this.correctStr + "<br>" +
           "Num Wrong: " + this.incorrect + ". Questions: " + this.incorrectStr + "<br>" +
           "Num Skipped: " + this.skipped + ". Questions: " + this.skippedStr + "<br>";
-          var numQuestions = this.renderedQuestionArray.length;
+          var numQuestions = this.score + this.incorrect + this.skipped;
           var percentCorrect = (this.score / numQuestions) * 100;
           scoreString += "Percent Correct: " + percentCorrect + "%";
           $(this.scoreDiv).html(scoreString);
           this.scoreDiv.style.display = "block";
       }
-      else 
+      else
       {
           var scoreString = "Num Correct: " + this.score + "<br>" +
           "Num Wrong: " + this.incorrect + "<br>" +
           "Num Skipped: " + this.skipped + "<br>";
-          var numQuestions = this.renderedQuestionArray.length;
+          var numQuestions = this.score + this.incorrect + this.skipped
           var percentCorrect = (this.score / numQuestions) * 100;
           scoreString += "Percent Correct: " + percentCorrect + "%";
           $(this.scoreDiv).html(scoreString);
@@ -639,7 +641,7 @@ Timed.prototype.displayScore = function () {
    }
    this.highlightNumberedList();
 };
-										
+
 Timed.prototype.highlightNumberedList = function () {
 	var correctCount = this.correctStr;
 	var	incorrectCount = this.incorrectStr;
@@ -648,24 +650,24 @@ Timed.prototype.highlightNumberedList = function () {
 	correctCount = correctCount.replace(/ /g,'').split(',');
 	incorrectCount = incorrectCount.replace(/ /g,'').split(',');
 	skippedCount = skippedCount.replace(/ /g,'').split(',');
-		
+
 	$(function () {		// This code is wrapped in a function so that it executes only after DOM has loaded
 		var numberedBtns = $("ul#pageNums > ul > li");
 		if (numberedBtns.hasClass("answered")) {
-			numberedBtns.removeClass("answered"); 
-		}	
+			numberedBtns.removeClass("answered");
+		}
 		for (var i = 0; i < correctCount.length; i++) {
-			var test = parseInt(correctCount[i])-1; 
-			numberedBtns.eq(parseInt(correctCount[i])-1).addClass("correctCount");	
+			var test = parseInt(correctCount[i])-1;
+			numberedBtns.eq(parseInt(correctCount[i])-1).addClass("correctCount");
 		}
 		for (var j = 0; j < incorrectCount.length; j++) {
-			numberedBtns.eq(parseInt(incorrectCount[j])-1).addClass("incorrectCount");	
+			numberedBtns.eq(parseInt(incorrectCount[j])-1).addClass("incorrectCount");
 		}
 		for (var k = 0; k < skippedCount.length; k++) {
-			numberedBtns.eq(parseInt(skippedCount[k])-1).addClass("skippedCount");	
-		} 
+			numberedBtns.eq(parseInt(skippedCount[k])-1).addClass("skippedCount");
+		}
 	});
-};	
+};
 
 
 /*=======================================================
diff --git a/runestone/assess/js/timedfitb.js b/runestone/assess/js/timedfitb.js
index 2ed5b04c5..555ff4e1b 100644
--- a/runestone/assess/js/timedfitb.js
+++ b/runestone/assess/js/timedfitb.js
@@ -35,7 +35,14 @@ TimedFITB.prototype.renderTimedIcon = function (component) {
 
 TimedFITB.prototype.checkCorrectTimed = function () {
     // Returns if the question was correct.    Used for timed assessment grading.
-    return this.correct;
+    switch (this.correct) {
+        case true:
+            return "T";
+        case false:
+            return "F";
+        default:
+            return null;
+    }
 };
 
 TimedFITB.prototype.hideFeedback = function () {
diff --git a/runestone/assess/js/timedmc.js b/runestone/assess/js/timedmc.js
index 8a1064c4b..e37f5aa9e 100644
--- a/runestone/assess/js/timedmc.js
+++ b/runestone/assess/js/timedmc.js
@@ -112,11 +112,25 @@ TimedMC.prototype.checkCorrectTimedMCMA = function () {
     } else if (this.givenArray.length !== 0) {
         this.correct = false;
     }
-    return this.correct;
+    switch (this.correct) {
+        case true:
+            return "T";
+        case false:
+            return "F";
+        default:
+            return null;
+    }
 };
 
 TimedMC.prototype.checkCorrectTimedMCMF = function () {
-    return this.correct;
+    switch (this.correct) {
+        case true:
+            return "T";
+        case false:
+            return "F";
+        default:
+            return null;
+    }
 };
 
 TimedMC.prototype.checkCorrectTimed = function () {
diff --git a/runestone/clickableArea/js/timedclickable.js b/runestone/clickableArea/js/timedclickable.js
index 286cac4d5..aae7ac769 100644
--- a/runestone/clickableArea/js/timedclickable.js
+++ b/runestone/clickableArea/js/timedclickable.js
@@ -36,7 +36,14 @@ TimedClickableArea.prototype.checkCorrectTimed = function () {
     if (this.correctNum === 0 && this.incorrectNum === 0) {
         this.correct = null;
     }
-    return this.correct;
+    switch (this.correct) {
+        case true:
+            return "T";
+        case false:
+            return "F";
+        default:
+            return null;
+    }
 };
 
 TimedClickableArea.prototype.hideFeedback = function () {
diff --git a/runestone/dragndrop/js/timeddnd.js b/runestone/dragndrop/js/timeddnd.js
index c3cdfca2d..49ab4959b 100644
--- a/runestone/dragndrop/js/timeddnd.js
+++ b/runestone/dragndrop/js/timeddnd.js
@@ -36,8 +36,14 @@ TimedDragNDrop.prototype.checkCorrectTimed = function () {
     if (this.unansweredNum === this.dragPairArray.length) {
         this.correct = null;
     }
-
-    return this.correct;
+    switch (this.correct) {
+        case true:
+            return "T";
+        case false:
+            return "F";
+        default:
+            return null;
+    }
 };
 
 TimedDragNDrop.prototype.hideFeedback = function () {

From 4852acebb291a7f75bd617d67a5ccf2c252ec713 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Fri, 8 Apr 2016 15:30:34 -0500
Subject: [PATCH 02/21] Removed unnecessary SA code that was causing bugs

---
 runestone/shortanswer/shortanswer.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/runestone/shortanswer/shortanswer.py b/runestone/shortanswer/shortanswer.py
index 4b98b22f6..c902f5f63 100755
--- a/runestone/shortanswer/shortanswer.py
+++ b/runestone/shortanswer/shortanswer.py
@@ -41,13 +41,8 @@ def __init__(self, options):
 
 def visit_journal_node(self, node):
     div_id = node.journalnode_components['divid']
-    back, subchapter = os.path.split(os.path.splitext(node.source.lower())[0])
-    back, chapter = os.path.split(back)
-    content = ''
     components = dict(node.journalnode_components)
-    components.update({'divid': div_id,
-                       'subchapter': subchapter,
-                       'chapter': chapter})
+    components.update({'divid': div_id})
     res = TEXT % components
     self.body.append(res)
 

From 7f4372fb42ed0feafb0b93dd6b22c332780d55b2 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Fri, 8 Apr 2016 15:53:43 -0500
Subject: [PATCH 03/21] Fixed small syntax bug

---
 runestone/assess/js/timedfitb.js             | 4 ++--
 runestone/assess/js/timedmc.js               | 4 ++--
 runestone/clickableArea/js/timedclickable.js | 4 ++--
 runestone/dragndrop/js/timeddnd.js           | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/runestone/assess/js/timedfitb.js b/runestone/assess/js/timedfitb.js
index 555ff4e1b..44f1ff7e8 100644
--- a/runestone/assess/js/timedfitb.js
+++ b/runestone/assess/js/timedfitb.js
@@ -36,9 +36,9 @@ TimedFITB.prototype.renderTimedIcon = function (component) {
 TimedFITB.prototype.checkCorrectTimed = function () {
     // Returns if the question was correct.    Used for timed assessment grading.
     switch (this.correct) {
-        case true:
+        case (true):
             return "T";
-        case false:
+        case (false):
             return "F";
         default:
             return null;
diff --git a/runestone/assess/js/timedmc.js b/runestone/assess/js/timedmc.js
index e37f5aa9e..877f31f70 100644
--- a/runestone/assess/js/timedmc.js
+++ b/runestone/assess/js/timedmc.js
@@ -124,9 +124,9 @@ TimedMC.prototype.checkCorrectTimedMCMA = function () {
 
 TimedMC.prototype.checkCorrectTimedMCMF = function () {
     switch (this.correct) {
-        case true:
+        case (true):
             return "T";
-        case false:
+        case (false):
             return "F";
         default:
             return null;
diff --git a/runestone/clickableArea/js/timedclickable.js b/runestone/clickableArea/js/timedclickable.js
index aae7ac769..526706d37 100644
--- a/runestone/clickableArea/js/timedclickable.js
+++ b/runestone/clickableArea/js/timedclickable.js
@@ -37,9 +37,9 @@ TimedClickableArea.prototype.checkCorrectTimed = function () {
         this.correct = null;
     }
     switch (this.correct) {
-        case true:
+        case (true):
             return "T";
-        case false:
+        case (false):
             return "F";
         default:
             return null;
diff --git a/runestone/dragndrop/js/timeddnd.js b/runestone/dragndrop/js/timeddnd.js
index 49ab4959b..7083a541f 100644
--- a/runestone/dragndrop/js/timeddnd.js
+++ b/runestone/dragndrop/js/timeddnd.js
@@ -37,9 +37,9 @@ TimedDragNDrop.prototype.checkCorrectTimed = function () {
         this.correct = null;
     }
     switch (this.correct) {
-        case true:
+        case (true):
             return "T";
-        case false:
+        case (false):
             return "F";
         default:
             return null;

From 662c03d6da3cb707b1fe289ac419f95f7232e218 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Fri, 8 Apr 2016 16:09:39 -0500
Subject: [PATCH 04/21] Added support for ignorable components in Timed

---
 runestone/assess/js/timed.js | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index 62245f2f8..269c81e51 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -311,6 +311,8 @@ Timed.prototype.createRenderedQuestionArray = function () {
             this.renderedQuestionArray.push(new TimedDragNDrop(opts));
         } else if ($(tmpChild).is("[data-component=clickablearea]")) {
             this.renderedQuestionArray.push(new TimedClickableArea(opts));
+        } else if ($(tmpChild).is("[data-component=shortanswer]")) {
+            this.renderedQuestionArray.push(new TimedShortAnswer(opts));
         }
     }
     if (this.random) {
@@ -520,7 +522,10 @@ Timed.prototype.finishAssessment = function () {
 
 Timed.prototype.submitTimedProblems = function (logFlag) {
     for (var i = 0; i < this.renderedQuestionArray.length; i++) {
-        this.renderedQuestionArray[i].processTimedSubmission(logFlag);
+        // Only try to check the answer if it's something automatically graded
+        if (this.renderedQuestionArray[i].ignoredTimedElement === undefined) {
+            this.renderedQuestionArray[i].processTimedSubmission(logFlag);
+        }
     }
     if (!this.showFeedback) {
         this.hideTimedFeedback();

From f791016cb672d26ad4567e9bb07203c9f70bf07e Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Sat, 9 Apr 2016 22:21:02 -0500
Subject: [PATCH 05/21] Added support for timed shortanswer questions

---
 runestone/assess/js/timed.js                  |  5 +-
 runestone/shortanswer/js/shortanswer.js       |  4 +-
 runestone/shortanswer/js/timed_shortanswer.js | 48 +++++++++++++++++++
 runestone/shortanswer/shortanswer.py          |  3 +-
 4 files changed, 53 insertions(+), 7 deletions(-)
 create mode 100644 runestone/shortanswer/js/timed_shortanswer.js

diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index 269c81e51..52077b3e9 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -522,10 +522,7 @@ Timed.prototype.finishAssessment = function () {
 
 Timed.prototype.submitTimedProblems = function (logFlag) {
     for (var i = 0; i < this.renderedQuestionArray.length; i++) {
-        // Only try to check the answer if it's something automatically graded
-        if (this.renderedQuestionArray[i].ignoredTimedElement === undefined) {
-            this.renderedQuestionArray[i].processTimedSubmission(logFlag);
-        }
+        this.renderedQuestionArray[i].processTimedSubmission(logFlag);
     }
     if (!this.showFeedback) {
         this.hideTimedFeedback();
diff --git a/runestone/shortanswer/js/shortanswer.js b/runestone/shortanswer/js/shortanswer.js
index cbc452241..936462025 100644
--- a/runestone/shortanswer/js/shortanswer.js
+++ b/runestone/shortanswer/js/shortanswer.js
@@ -179,7 +179,9 @@ ShortAnswer.prototype.loadJournal = function () {
 =================================*/
 $(document).ready(function () {
     $("[data-component=shortanswer]").each(function (index) {
-        saList[this.id] = new ShortAnswer({"orig": this, 'useRunestoneServices': eBookConfig.useRunestoneServices});
+        if ($(this.parentNode).data("component") !== "timedAssessment") { // If this element exists within a timed component, don't render it here
+            saList[this.id] = new ShortAnswer({"orig": this, 'useRunestoneServices': eBookConfig.useRunestoneServices});
+        }
     });
 
 });
diff --git a/runestone/shortanswer/js/timed_shortanswer.js b/runestone/shortanswer/js/timed_shortanswer.js
new file mode 100644
index 000000000..5a3fffdb9
--- /dev/null
+++ b/runestone/shortanswer/js/timed_shortanswer.js
@@ -0,0 +1,48 @@
+function TimedShortAnswer (opts) {
+    if (opts) {
+        this.timedInit(opts);
+    }
+}
+TimedShortAnswer.prototype = new ShortAnswer();
+
+TimedShortAnswer.prototype.timedInit = function (opts) {
+    this.init(opts);
+    this.ignoredTimedElement = true;
+    this.renderTimedIcon(this.containerDiv);
+    this.hideButtons();
+};
+
+
+TimedShortAnswer.prototype.hideButtons = function () {
+    $(this.submitButton).hide();
+
+};
+
+TimedShortAnswer.prototype.renderTimedIcon = function (component) {
+    // renders the clock icon on timed components.    The component parameter
+    // is the element that the icon should be appended to.
+    var timeIconDiv = document.createElement("div");
+    var timeIcon = document.createElement("img");
+    $(timeIcon).attr({
+        "src": "../_static/clock.png",
+        "style": "width:15px;height:15px"
+    });
+    timeIconDiv.className = "timeTip";
+    timeIconDiv.title = "";
+    timeIconDiv.appendChild(timeIcon);
+    $(component).prepend(timeIconDiv);
+};
+
+TimedShortAnswer.prototype.checkCorrectTimed = function () {
+    // Returns if the question was correct.    Used for timed assessment grading.
+    return "I";   // we ignore this in the grading
+};
+
+TimedShortAnswer.prototype.hideFeedback = function () {
+    $(this.feedbackDiv).hide();
+};
+
+TimedShortAnswer.prototype.processTimedSubmission = function () {
+    this.submitJournal();
+    this.jTextArea.disabled = true;
+};
diff --git a/runestone/shortanswer/shortanswer.py b/runestone/shortanswer/shortanswer.py
index c902f5f63..817b049e9 100755
--- a/runestone/shortanswer/shortanswer.py
+++ b/runestone/shortanswer/shortanswer.py
@@ -24,10 +24,9 @@
 
 def setup(app):
     app.add_directive('shortanswer', JournalDirective)
-
     app.add_node(JournalNode, html=(visit_journal_node, depart_journal_node))
-
     app.add_javascript('shortanswer.js')
+    app.add_javascript('timed_shortanswer.js')
 
 
 TEXT = """

From d9f11fcf90f065e97369b3865ff820985bae140c Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Sun, 10 Apr 2016 13:27:24 -0500
Subject: [PATCH 06/21] Don't need ignoredTimed property anymore

---
 runestone/shortanswer/js/timed_shortanswer.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/runestone/shortanswer/js/timed_shortanswer.js b/runestone/shortanswer/js/timed_shortanswer.js
index 5a3fffdb9..d00f9e591 100644
--- a/runestone/shortanswer/js/timed_shortanswer.js
+++ b/runestone/shortanswer/js/timed_shortanswer.js
@@ -7,7 +7,6 @@ TimedShortAnswer.prototype = new ShortAnswer();
 
 TimedShortAnswer.prototype.timedInit = function (opts) {
     this.init(opts);
-    this.ignoredTimedElement = true;
     this.renderTimedIcon(this.containerDiv);
     this.hideButtons();
 };
@@ -34,7 +33,6 @@ TimedShortAnswer.prototype.renderTimedIcon = function (component) {
 };
 
 TimedShortAnswer.prototype.checkCorrectTimed = function () {
-    // Returns if the question was correct.    Used for timed assessment grading.
     return "I";   // we ignore this in the grading
 };
 

From 05a2f4b57f038fab826b3dd8953480efd2a7b1cb Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Sun, 10 Apr 2016 13:38:45 -0500
Subject: [PATCH 07/21] Updated comments

---
 runestone/assess/js/timedfitb.js              | 3 ++-
 runestone/assess/js/timedmc.js                | 6 ++++--
 runestone/clickableArea/js/timedclickable.js  | 5 +++--
 runestone/dragndrop/js/timeddnd.js            | 1 +
 runestone/shortanswer/js/timed_shortanswer.js | 1 +
 5 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/runestone/assess/js/timedfitb.js b/runestone/assess/js/timedfitb.js
index 44f1ff7e8..664fa4826 100644
--- a/runestone/assess/js/timedfitb.js
+++ b/runestone/assess/js/timedfitb.js
@@ -34,7 +34,7 @@ TimedFITB.prototype.renderTimedIcon = function (component) {
 };
 
 TimedFITB.prototype.checkCorrectTimed = function () {
-    // Returns if the question was correct.    Used for timed assessment grading.
+    // Returns if the question was correct, incorrect, or skipped (return null in the last case)
     switch (this.correct) {
         case (true):
             return "T";
@@ -53,6 +53,7 @@ TimedFITB.prototype.hideFeedback = function () {
 };
 
 TimedFITB.prototype.processTimedSubmission = function () {
+    // Disable input, then evaluate component
     for (var i = 0; i < this.blankArray.length; i++) {
         this.blankArray[i].disabled = true;
     }
diff --git a/runestone/assess/js/timedmc.js b/runestone/assess/js/timedmc.js
index 877f31f70..43b406d38 100644
--- a/runestone/assess/js/timedmc.js
+++ b/runestone/assess/js/timedmc.js
@@ -113,9 +113,9 @@ TimedMC.prototype.checkCorrectTimedMCMA = function () {
         this.correct = false;
     }
     switch (this.correct) {
-        case true:
+        case (true):
             return "T";
-        case false:
+        case (false):
             return "F";
         default:
             return null;
@@ -123,6 +123,7 @@ TimedMC.prototype.checkCorrectTimedMCMA = function () {
 };
 
 TimedMC.prototype.checkCorrectTimedMCMF = function () {
+    // Returns if the question was correct, incorrect, or skipped (return null in the last case)
     switch (this.correct) {
         case (true):
             return "T";
@@ -148,6 +149,7 @@ TimedMC.prototype.hideFeedback = function () {
 };
 
 TimedMC.prototype.processTimedSubmission = function (logFlag) {
+    // Disable input, then evaluate component
     for (var i = 0; i < this.optionArray.length; i++) {
         this.optionArray[i]["input"].disabled = true;
     }
diff --git a/runestone/clickableArea/js/timedclickable.js b/runestone/clickableArea/js/timedclickable.js
index 526706d37..c652b4324 100644
--- a/runestone/clickableArea/js/timedclickable.js
+++ b/runestone/clickableArea/js/timedclickable.js
@@ -32,7 +32,7 @@ TimedClickableArea.prototype.renderTimedIcon = function (component) {
 };
 
 TimedClickableArea.prototype.checkCorrectTimed = function () {
-    // Returns if the question was correct.    Used for timed assessment grading.
+    // Returns if the question was correct, incorrect, or skipped (return null in the last case)
     if (this.correctNum === 0 && this.incorrectNum === 0) {
         this.correct = null;
     }
@@ -51,11 +51,12 @@ TimedClickableArea.prototype.hideFeedback = function () {
 };
 
 TimedClickableArea.prototype.processTimedSubmission = function () {
+    // Disable input, then evaluate component
     for (var i = 0; i < this.clickableArray.length; i++) {
         $(this.clickableArray[i]).css("cursor", "initial");
         this.clickableArray[i].onclick = function () {
             return;
-        }
+        };
     }
     this.clickableEval();
 };
diff --git a/runestone/dragndrop/js/timeddnd.js b/runestone/dragndrop/js/timeddnd.js
index 7083a541f..4ea0de2ff 100644
--- a/runestone/dragndrop/js/timeddnd.js
+++ b/runestone/dragndrop/js/timeddnd.js
@@ -51,6 +51,7 @@ TimedDragNDrop.prototype.hideFeedback = function () {
 };
 
 TimedDragNDrop.prototype.processTimedSubmission = function () {
+    // Disable input & evaluate component
     $(this.resetButton).hide();
     this.dragEval();
     for (var i = 0; i < this.dragPairArray.length; i++) {   // No more dragging
diff --git a/runestone/shortanswer/js/timed_shortanswer.js b/runestone/shortanswer/js/timed_shortanswer.js
index d00f9e591..aa1484de4 100644
--- a/runestone/shortanswer/js/timed_shortanswer.js
+++ b/runestone/shortanswer/js/timed_shortanswer.js
@@ -41,6 +41,7 @@ TimedShortAnswer.prototype.hideFeedback = function () {
 };
 
 TimedShortAnswer.prototype.processTimedSubmission = function () {
+    // Disable input & evaluate component
     this.submitJournal();
     this.jTextArea.disabled = true;
 };

From 63a866aee19428c3aa751b29d38180096a61876c Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Sun, 10 Apr 2016 14:08:40 -0500
Subject: [PATCH 08/21] Fixed grading bug in FITB

---
 runestone/assess/js/fitb.js | 37 +++++++++++++++----------------------
 1 file changed, 15 insertions(+), 22 deletions(-)

diff --git a/runestone/assess/js/fitb.js b/runestone/assess/js/fitb.js
index 41640494a..b69a1149d 100644
--- a/runestone/assess/js/fitb.js
+++ b/runestone/assess/js/fitb.js
@@ -11,26 +11,6 @@
 ===                6/4/15                ===
 ==========================================*/
 
-/*=======================================
-===         Global functions          ===
-=== (used by more than one component) ===
-=======================================*/
-
-var feedBack = function (elem, correct, feedbackText) {        // Displays feedback on page--miscellaneous function that can be used by multple objects
-    // elem is the Element in which to put the feedback
-    if (correct) {
-        $(elem).html("You are Correct!");
-        $(elem).attr("class", "alert alert-success");
-    } else {
-        if (feedbackText === null) {
-            feedbackText = "";
-        }
-        $(elem).html("Incorrect.    " + feedbackText);
-        $(elem).attr("class", "alert alert-danger");
-    }
-};
-
-
 /*==================================================
 == Begin code for the Fill In The Blank component ==
 ==================================================*/
@@ -247,7 +227,7 @@ FITB.prototype.enableCompareButton = function () {
 FITB.prototype.checkFITBStorage = function () {
     this.isCorrectArray = [];
     this.displayFeed = [];
-    // Starts chain of functions which ends with feedBack() displaying feedback to user
+    // Starts chain of functions which ends with displaying feedback to user
     this.evaluateAnswers();
     this.renderFITBFeedback();
     var answerInfo = "answer:" + this.given_arr + ":" + (this.correct ? "correct" : "no");
@@ -278,12 +258,25 @@ FITB.prototype.evaluateAnswers = function () {
     }
     if ($.inArray("", this.isCorrectArray) < 0 && $.inArray(false, this.isCorrectArray) < 0) {
         this.correct = true;
-    } else if ($.inArray(false, this.isCorrectArray) >= 0 && $.inArray("", this.isCorrectArray) < 0) {
+    } else if (this.isCompletelyBlank()) {
+        this.correct = null;
+    } else {
         this.correct = false;
     }
+    console.log(this.correct);
     localStorage.setItem(eBookConfig.email + ":" + this.divid + "-given", this.given_arr.join(";"));
 };
 
+FITB.prototype.isCompletelyBlank = function () {
+    // Returns true if the user didn't fill in any of the blanks, else false
+    for (var i = 0; i < this.isCorrectArray.length; i++) {
+        if (this.isCorrectArray[i] !== "") {
+            return false;
+        }
+    }
+    return true;
+};
+
 FITB.prototype.populateDisplayFeed = function (index, given) {
     var fbl = this.feedbackArray[index];
     for (var j = 0; j < fbl.length; j++) {

From de51664691eeeb7b50241614ca75505172e1ee6f Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Thu, 28 Apr 2016 23:22:43 -0500
Subject: [PATCH 09/21] Added support for timed parsons questions

---
 runestone/parsons/css/parsons.css     |  4 ++
 runestone/parsons/js/parsons_setup.js | 20 ++++-----
 runestone/parsons/js/timedparsons.js  | 61 +++++++++++++++++++++++++++
 runestone/parsons/parsons.py          |  3 +-
 4 files changed, 77 insertions(+), 11 deletions(-)
 create mode 100644 runestone/parsons/js/timedparsons.js

diff --git a/runestone/parsons/css/parsons.css b/runestone/parsons/css/parsons.css
index 7dcb5fef2..837dbd67f 100644
--- a/runestone/parsons/css/parsons.css
+++ b/runestone/parsons/css/parsons.css
@@ -135,3 +135,7 @@ li.correctPosition, .testcase.pass {
 	margin-right: auto;
 	text-align:center;
 }
+
+.parsons-disabled {
+    pointer-events: none;
+}
diff --git a/runestone/parsons/js/parsons_setup.js b/runestone/parsons/js/parsons_setup.js
index be2146a79..9be0effea 100644
--- a/runestone/parsons/js/parsons_setup.js
+++ b/runestone/parsons/js/parsons_setup.js
@@ -93,28 +93,28 @@ Parsons.prototype.formatCode = function () {
 == Creating/appending new HTML tags ==
 ====================================*/
 Parsons.prototype.createParsonsView = function () {         // Create DOM elements
-    this.containingDiv = document.createElement("div");
-    $(this.containingDiv).addClass("parsons alert alert-warning");
-    this.containingDiv.id = "parsons-" + this.counterId;
+    this.containerDiv = document.createElement("div");
+    $(this.containerDiv).addClass("parsons alert alert-warning");
+    this.containerDiv.id = "parsons-" + this.counterId;
 
     this.parsTextDiv = document.createElement("div");
     $(this.parsTextDiv).addClass("parsons-text");
     this.parsTextDiv.innerHTML = this.question.innerHTML;
-    this.containingDiv.appendChild(this.parsTextDiv);
+    this.containerDiv.appendChild(this.parsTextDiv);
 
     this.leftClearDiv = document.createElement("div");
     this.leftClearDiv.style["clear"] = "left";
-    this.containingDiv.appendChild(this.leftClearDiv);
+    this.containerDiv.appendChild(this.leftClearDiv);
 
     this.origDiv = document.createElement("div");
     this.origDiv.id = "parsons-orig-" + this.counterId;
     this.origDiv.style["display"] = "none";
     this.origDiv.innerHTML = this.fmtCode;
-    this.containingDiv.appendChild(this.origDiv);
+    this.containerDiv.appendChild(this.origDiv);
 
     this.sortContainerDiv = document.createElement("div");
     $(this.sortContainerDiv).addClass("sortable-code-container");
-    this.containingDiv.appendChild(this.sortContainerDiv);
+    this.containerDiv.appendChild(this.sortContainerDiv);
 
     this.sortTrashDiv = document.createElement("div");
     this.sortTrashDiv.id = "parsons-sortableTrash-" + this.counterId;
@@ -132,7 +132,7 @@ Parsons.prototype.createParsonsView = function () {         // Create DOM elemen
 
     this.parsonsControlDiv = document.createElement("div");
     $(this.parsonsControlDiv).addClass("parsons-controls");
-    this.containingDiv.appendChild(this.parsonsControlDiv);
+    this.containerDiv.appendChild(this.parsonsControlDiv);
 
     this.checkButt = document.createElement("button");
     $(this.checkButt).attr("class", "btn btn-success");
@@ -153,7 +153,7 @@ Parsons.prototype.createParsonsView = function () {         // Create DOM elemen
     this.parsonsControlDiv.appendChild(this.messageDiv);
     $(this.messageDiv).hide();
 
-    $(this.origElem).replaceWith(this.containingDiv);
+    $(this.origElem).replaceWith(this.containerDiv);
 
     this.createParsonsWidget();
 };
@@ -270,7 +270,7 @@ Parsons.prototype.tryLocalStorage = function () {
 $(document).ready(function () {
     $pjQ("[data-component=parsons]").each(function (index) {
         if ($(this.parentNode).data("component") != "timedAssessment") {
-           prsList[this.id] = new Parsons({"orig": this});
+           prsList[this.id] = new Parsons({"orig": this, "useRunestoneServices": eBookConfig.useRunestoneServices});
         }
     });
 
diff --git a/runestone/parsons/js/timedparsons.js b/runestone/parsons/js/timedparsons.js
new file mode 100644
index 000000000..86a55dd51
--- /dev/null
+++ b/runestone/parsons/js/timedparsons.js
@@ -0,0 +1,61 @@
+function TimedParsons (opts) {
+    if (opts) {
+        this.timedInit(opts);
+    }
+}
+
+TimedParsons.prototype = new Parsons();
+
+TimedParsons.prototype.timedInit = function (opts) {
+    this.init(opts);
+    this.renderTimedIcon(this.containerDiv);
+    this.hideButtons();
+};
+
+
+TimedParsons.prototype.hideButtons = function () {
+    $(this.checkButt).hide();
+};
+
+TimedParsons.prototype.renderTimedIcon = function (component) {
+    // renders the clock icon on timed components.    The component parameter
+    // is the element that the icon should be appended to.
+    var timeIconDiv = document.createElement("div");
+    var timeIcon = document.createElement("img");
+    $(timeIcon).attr({
+        "src": "../_static/clock.png",
+        "style": "width:15px;height:15px"
+    });
+    timeIconDiv.className = "timeTip";
+    timeIconDiv.title = "";
+    timeIconDiv.appendChild(timeIcon);
+    $(component).prepend(timeIconDiv);
+};
+
+TimedParsons.prototype.checkCorrectTimed = function () {
+    return this.correct ? "T" : "F";
+};
+
+TimedParsons.prototype.hideFeedback = function () {
+    $(this.messageDiv).hide();
+};
+
+TimedParsons.prototype.processTimedSubmission = function () {
+    // Disable input & evaluate component
+    var hash = this.pwidget.getHash("#ul-parsons-sortableCode-" + this.counterId);
+    localStorage.setItem(this.divid, hash);
+    hash = this.pwidget.getHash("#ul-parsons-sortableTrash-" + this.counterId);
+    localStorage.setItem(this.divid + "-trash", hash);
+    this.pwidget.getFeedback();
+
+    // Gross way to check if it's correct or not, but it's better than modifying the 3rd party parsons code to include a "correct" variable
+    if ($(this.messageDiv).hasClass("alert-success")) {
+        this.correct = true;
+    } else {
+        this.correct = false;
+    }
+
+    this.resetButt.disabled = true;
+    $(this.sortContainerDiv).addClass("parsons-disabled");
+
+};
diff --git a/runestone/parsons/parsons.py b/runestone/parsons/parsons.py
index 00c7dd887..36e3fecd3 100644
--- a/runestone/parsons/parsons.py
+++ b/runestone/parsons/parsons.py
@@ -37,6 +37,7 @@ def setup(app):
     app.add_javascript('parsons_setup.js')
     app.add_javascript('parsons.js')
     app.add_javascript('parsons-noconflict.js')
+    app.add_javascript('timedparsons.js')
 
 class ParsonsProblem(Assessment):
     required_arguments = 1
@@ -88,7 +89,7 @@ def findmax(alist):
         self.options['qnumber'] = self.getNumber()
         self.options['instructions'] = ""
         self.options['code'] = self.content
-          
+
         if 'maxdist' not in self.options:
             self.options['maxdist'] = '3'
         if '-----' in self.content:

From df5282e47216ae748dea4a0ab3e9f71b56b9dcee Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Thu, 28 Apr 2016 23:27:08 -0500
Subject: [PATCH 10/21] Removed console.logs

---
 runestone/assess/js/fitb.js  | 1 -
 runestone/assess/js/timed.js | 4 ++++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/runestone/assess/js/fitb.js b/runestone/assess/js/fitb.js
index b69a1149d..86ae5bcae 100644
--- a/runestone/assess/js/fitb.js
+++ b/runestone/assess/js/fitb.js
@@ -263,7 +263,6 @@ FITB.prototype.evaluateAnswers = function () {
     } else {
         this.correct = false;
     }
-    console.log(this.correct);
     localStorage.setItem(eBookConfig.email + ":" + this.divid + "-given", this.given_arr.join(";"));
 };
 
diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index 52077b3e9..a072a97c0 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -313,6 +313,8 @@ Timed.prototype.createRenderedQuestionArray = function () {
             this.renderedQuestionArray.push(new TimedClickableArea(opts));
         } else if ($(tmpChild).is("[data-component=shortanswer]")) {
             this.renderedQuestionArray.push(new TimedShortAnswer(opts));
+        } else if ($(tmpChild).is("[data-component=parsons]")) {
+            this.renderedQuestionArray.push(new TimedParsons(opts));
         }
     }
     if (this.random) {
@@ -335,6 +337,8 @@ Timed.prototype.randomizeRQA = function () {
 };
 
 Timed.prototype.renderTimedQuestion = function () {
+    console.log(this.renderedQuestionArray);
+    console.log(this.currentQuestionIndex);
     $(this.switchDiv).replaceWith(this.renderedQuestionArray[this.currentQuestionIndex].containerDiv);
     this.switchDiv = this.renderedQuestionArray[this.currentQuestionIndex].containerDiv;
 };

From 9a894075f656d8d753d9cbde16a7075d1bcf8b0d Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Thu, 28 Apr 2016 23:56:11 -0500
Subject: [PATCH 11/21] First version of timed activecode

---
 runestone/activecode/activecode.py          |  1 +
 runestone/activecode/css/activecode.css     |  6 ++-
 runestone/activecode/js/activecode.js       | 28 ++++++------
 runestone/activecode/js/timed_activecode.js | 49 +++++++++++++++++++++
 runestone/assess/js/timed.js                |  4 +-
 5 files changed, 72 insertions(+), 16 deletions(-)
 create mode 100644 runestone/activecode/js/timed_activecode.js

diff --git a/runestone/activecode/activecode.py b/runestone/activecode/activecode.py
index 987bbbf77..42b38c10d 100644
--- a/runestone/activecode/activecode.py
+++ b/runestone/activecode/activecode.py
@@ -47,6 +47,7 @@ def setup(app):
     app.add_javascript('skulpt.min.js')
     app.add_javascript('skulpt-stdlib.js')
     app.add_javascript('clike.js')
+    app.add_javascript('timed_activecode.js')
 
     app.add_node(ActivcodeNode, html=(visit_ac_node, depart_ac_node))
 
diff --git a/runestone/activecode/css/activecode.css b/runestone/activecode/css/activecode.css
index 7fbb6a54e..84b419e38 100644
--- a/runestone/activecode/css/activecode.css
+++ b/runestone/activecode/css/activecode.css
@@ -94,4 +94,8 @@
 
 .full_width ol {
 	max-width: 100% !important;
-}
\ No newline at end of file
+}
+
+.ac-disabled {
+	pointer-events: none;
+}
diff --git a/runestone/activecode/js/activecode.js b/runestone/activecode/js/activecode.js
index 3c8391260..7c0812881 100755
--- a/runestone/activecode/js/activecode.js
+++ b/runestone/activecode/js/activecode.js
@@ -64,23 +64,23 @@ ActiveCode.prototype.init = function(opts) {
 };
 
 ActiveCode.prototype.createEditor = function (index) {
-    var newdiv = document.createElement('div');
+    this.containerDiv = document.createElement('div');
     var linkdiv = document.createElement('div')
     linkdiv.id = this.divid.replace(/_/g,'-').toLowerCase();  // :ref: changes _ to - so add this as a target
-    $(newdiv).addClass("ac_section alert alert-warning");
+    $(this.containerDiv).addClass("ac_section alert alert-warning");
     var codeDiv = document.createElement("div");
     $(codeDiv).addClass("ac_code_div col-md-12");
     this.codeDiv = codeDiv;
-    newdiv.id = this.divid;
-    newdiv.lang = this.language;
-    this.outerDiv = newdiv;
+    this.containerDiv.id = this.divid;
+    this.containerDiv.lang = this.language;
+    this.outerDiv = this.containerDiv;
 
-    $(this.origElem).replaceWith(newdiv);
+    $(this.origElem).replaceWith(this.containerDiv);
     if (linkdiv.id !== this.divid) {  // Don't want the 'extra' target if they match.
-        newdiv.appendChild(linkdiv);
+        this.containerDiv.appendChild(linkdiv);
     }
-    newdiv.appendChild(codeDiv);
-    var editor = CodeMirror(codeDiv, {value: this.code, lineNumbers: true, mode: newdiv.lang});
+    this.containerDiv.appendChild(codeDiv);
+    var editor = CodeMirror(codeDiv, {value: this.code, lineNumbers: true, mode: this.containerDiv.lang});
 
     // Make the editor resizable
     $(editor.getWrapperElement()).resizable({
@@ -727,7 +727,7 @@ JSActiveCode.prototype.runProg = function() {
         if (!str) str="";
         _this.output.innerHTML += _this.outputfun(str)+"<br />";
             };
-    
+
     $(this.eContainer).remove();
     $(this.output).text('');
     $(this.codeDiv).switchClass("col-md-12","col-md-6",{duration:500,queue:false});
@@ -997,8 +997,8 @@ AudioTour.prototype.tour = function (divid, audio_type, bcount) {
         // str+="<audio id="+akey+" preload='auto'><source src='http://ice-web.cc.gatech.edu/ce21/audio/"+
         // akey+".mp3' type='audio/mpeg'><source src='http://ice-web.cc.gatech.edu/ce21/audio/"+akey+
         // ".ogg' type='audio/ogg'>Your browser does not support the audio tag</audio>";
-        
-        var dir = "http://media.interactivepython.org/" + eBookConfig.basecourse + "/audio/" 
+
+        var dir = "http://media.interactivepython.org/" + eBookConfig.basecourse + "/audio/"
         //var dir = "../_static/audio/"
         str += "<audio id=" + akey + " preload='auto' >";
         str += "<source src='" + dir + akey + ".wav' type='audio/wav'>";
@@ -1591,7 +1591,9 @@ ACFactory.toggleScratchActivecode = function () {
 $(document).ready(function() {
     ACFactory.createScratchActivecode();
     $('[data-component=activecode]').each( function(index ) {
-        edList[this.id] = ACFactory.createActiveCode(this, $(this).data('lang'));
+        if ($(this.parentNode).data("component") !== "timedAssessment") {   // If this element exists within a timed component, don't render it here
+            edList[this.id] = ACFactory.createActiveCode(this, $(this).data('lang'));
+        }
     });
     if (loggedout) {
         for (k in edList) {
diff --git a/runestone/activecode/js/timed_activecode.js b/runestone/activecode/js/timed_activecode.js
new file mode 100644
index 000000000..fff7554ed
--- /dev/null
+++ b/runestone/activecode/js/timed_activecode.js
@@ -0,0 +1,49 @@
+function TimedActiveCode (opts) {
+    if (opts) {
+        this.timedInit(opts);
+    }
+}
+TimedActiveCode.prototype = new ActiveCode();
+
+TimedActiveCode.prototype.timedInit = function (opts) {
+    this.init(opts);
+    this.renderTimedIcon(this.containerDiv);
+    this.hideButtons();
+};
+
+
+TimedActiveCode.prototype.hideButtons = function () {
+    $(this.saveButton).hide();
+    $(this.loadButton).hide();
+
+};
+
+TimedActiveCode.prototype.renderTimedIcon = function (component) {
+    // renders the clock icon on timed components.    The component parameter
+    // is the element that the icon should be appended to.
+    var timeIconDiv = document.createElement("div");
+    var timeIcon = document.createElement("img");
+    $(timeIcon).attr({
+        "src": "../_static/clock.png",
+        "style": "width:15px;height:15px"
+    });
+    timeIconDiv.className = "timeTip";
+    timeIconDiv.title = "";
+    timeIconDiv.appendChild(timeIcon);
+    $(component).prepend(timeIconDiv);
+};
+
+TimedActiveCode.prototype.checkCorrectTimed = function () {
+    return "I";   // we ignore this in the grading
+};
+
+TimedActiveCode.prototype.hideFeedback = function () {
+    // no feedback to hide
+};
+
+TimedActiveCode.prototype.processTimedSubmission = function () {
+    // Disable input & evaluate component
+    this.saveEditor();
+    this.runButton.disabled = true;
+    $(this.codeDiv).addClass("ac-disabled");
+};
diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index a072a97c0..85a881a25 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -315,6 +315,8 @@ Timed.prototype.createRenderedQuestionArray = function () {
             this.renderedQuestionArray.push(new TimedShortAnswer(opts));
         } else if ($(tmpChild).is("[data-component=parsons]")) {
             this.renderedQuestionArray.push(new TimedParsons(opts));
+        } else if ($(tmpChild).is("[data-component=activecode]")) {
+            this.renderedQuestionArray.push(new TimedActiveCode(opts));
         }
     }
     if (this.random) {
@@ -337,8 +339,6 @@ Timed.prototype.randomizeRQA = function () {
 };
 
 Timed.prototype.renderTimedQuestion = function () {
-    console.log(this.renderedQuestionArray);
-    console.log(this.currentQuestionIndex);
     $(this.switchDiv).replaceWith(this.renderedQuestionArray[this.currentQuestionIndex].containerDiv);
     this.switchDiv = this.renderedQuestionArray[this.currentQuestionIndex].containerDiv;
 };

From cd4c393fdacfdebfdc202cda6a8920e0a1fe85aa Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Fri, 29 Apr 2016 13:12:29 -0500
Subject: [PATCH 12/21] Fixed timed activecode bugs

---
 runestone/activecode/js/activecode.js       |  2 ++
 runestone/activecode/js/timed_activecode.js | 11 +++++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/runestone/activecode/js/activecode.js b/runestone/activecode/js/activecode.js
index 7c0812881..83f9d1f7a 100755
--- a/runestone/activecode/js/activecode.js
+++ b/runestone/activecode/js/activecode.js
@@ -199,6 +199,8 @@ ActiveCode.prototype.createControls = function () {
         $(butt).click((function() {new AudioTour(this.divid, this.editor.getValue(), 1, $(this.origElem).data("audio"))}).bind(this));
     }
 
+    console.log("HERE");
+
     $(this.outerDiv).prepend(ctrlDiv);
 
 };
diff --git a/runestone/activecode/js/timed_activecode.js b/runestone/activecode/js/timed_activecode.js
index fff7554ed..659313845 100644
--- a/runestone/activecode/js/timed_activecode.js
+++ b/runestone/activecode/js/timed_activecode.js
@@ -13,9 +13,11 @@ TimedActiveCode.prototype.timedInit = function (opts) {
 
 
 TimedActiveCode.prototype.hideButtons = function () {
-    $(this.saveButton).hide();
-    $(this.loadButton).hide();
-
+    var buttonList = [this.saveButton, this.loadButton, this.gradeButton, this.showHideButt, this.clButton, this.coachButton, this.atButton];
+    for (var i = 0; i < buttonList.length; i++) {
+        if (buttonList[i] !== undefined && buttonList[i] !== null)
+            $(buttonList[i]).hide();
+    }
 };
 
 TimedActiveCode.prototype.renderTimedIcon = function (component) {
@@ -43,7 +45,8 @@ TimedActiveCode.prototype.hideFeedback = function () {
 
 TimedActiveCode.prototype.processTimedSubmission = function () {
     // Disable input & evaluate component
-    this.saveEditor();
+    if (this.useRunestoneServies)
+        this.saveEditor();
     this.runButton.disabled = true;
     $(this.codeDiv).addClass("ac-disabled");
 };

From beb89dcdf36df4d31720b7e01c66c15347a114d0 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Fri, 29 Apr 2016 13:49:49 -0500
Subject: [PATCH 13/21] Fixed local storage bug in timed parsons

---
 runestone/assess/js/timed.js         | 2 +-
 runestone/parsons/js/timedparsons.js | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index 85a881a25..36238d6a7 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -356,7 +356,7 @@ Timed.prototype.handlePrevAssessment = function () {
         this.done = 1;
         $(this.timedDiv).show();
         this.submitTimedProblems(false); // do not log these results
-}
+};
 
 Timed.prototype.startAssessment = function () {
     this.tookTimedExam();
diff --git a/runestone/parsons/js/timedparsons.js b/runestone/parsons/js/timedparsons.js
index 86a55dd51..850d40324 100644
--- a/runestone/parsons/js/timedparsons.js
+++ b/runestone/parsons/js/timedparsons.js
@@ -40,12 +40,14 @@ TimedParsons.prototype.hideFeedback = function () {
     $(this.messageDiv).hide();
 };
 
-TimedParsons.prototype.processTimedSubmission = function () {
+TimedParsons.prototype.processTimedSubmission = function (logflag) {
     // Disable input & evaluate component
     var hash = this.pwidget.getHash("#ul-parsons-sortableCode-" + this.counterId);
-    localStorage.setItem(this.divid, hash);
+    if (logflag)
+        localStorage.setItem(this.divid, hash);
     hash = this.pwidget.getHash("#ul-parsons-sortableTrash-" + this.counterId);
-    localStorage.setItem(this.divid + "-trash", hash);
+    if (logflag)
+        localStorage.setItem(this.divid + "-trash", hash);
     this.pwidget.getFeedback();
 
     // Gross way to check if it's correct or not, but it's better than modifying the 3rd party parsons code to include a "correct" variable

From 5a1483a945474d55da04ffc4aba751c769560b61 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Fri, 29 Apr 2016 17:13:57 -0500
Subject: [PATCH 14/21] Removed extraneous console log

---
 runestone/activecode/js/activecode.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/runestone/activecode/js/activecode.js b/runestone/activecode/js/activecode.js
index 83f9d1f7a..6e6dd89c2 100755
--- a/runestone/activecode/js/activecode.js
+++ b/runestone/activecode/js/activecode.js
@@ -199,7 +199,6 @@ ActiveCode.prototype.createControls = function () {
         $(butt).click((function() {new AudioTour(this.divid, this.editor.getValue(), 1, $(this.origElem).data("audio"))}).bind(this));
     }
 
-    console.log("HERE");
 
     $(this.outerDiv).prepend(ctrlDiv);
 

From c55f94d6ace5912677c285c5d8fb3482f1ec2203 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Sun, 1 May 2016 14:42:09 -0500
Subject: [PATCH 15/21] Fixed loading/running from storage after timed submit
 in activecode

---
 runestone/activecode/js/activecode.js       |  8 +++++---
 runestone/activecode/js/timed_activecode.js | 11 ++++++++---
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/runestone/activecode/js/activecode.js b/runestone/activecode/js/activecode.js
index 6e6dd89c2..0125e816c 100755
--- a/runestone/activecode/js/activecode.js
+++ b/runestone/activecode/js/activecode.js
@@ -323,11 +323,9 @@ ActiveCode.prototype.saveEditor = function () {
 };
 
 ActiveCode.prototype.loadEditor = function () {
-
     var loadEditor = (function (data, status, whatever) {
         // function called when contents of database are returned successfully
         var res = eval(data)[0];
-
         if (res.source) {
             this.editor.setValue(res.source);
             setTimeout(function() {
@@ -353,8 +351,12 @@ ActiveCode.prototype.loadEditor = function () {
     if (this.sid !== undefined) {
         data['sid'] = this.sid;
     }
+    // This function needs to be chainable for when we want to do things like run the activecode
+    // immediately after loading the previous input (such as in a timed exam)
+    var dfd = jQuery.Deferred();
     this.logBookEvent({'event': 'activecode', 'act': 'load', 'div_id': this.divid}); // Log the run event
-    jQuery.get(eBookConfig.ajaxURL + 'getprog', data, loadEditor);
+    jQuery.get(eBookConfig.ajaxURL + 'getprog', data, loadEditor).done(function () {dfd.resolve();});
+    return dfd;
 
 };
 
diff --git a/runestone/activecode/js/timed_activecode.js b/runestone/activecode/js/timed_activecode.js
index 659313845..08e454095 100644
--- a/runestone/activecode/js/timed_activecode.js
+++ b/runestone/activecode/js/timed_activecode.js
@@ -43,10 +43,15 @@ TimedActiveCode.prototype.hideFeedback = function () {
     // no feedback to hide
 };
 
-TimedActiveCode.prototype.processTimedSubmission = function () {
+TimedActiveCode.prototype.processTimedSubmission = function (logFlag) {
     // Disable input & evaluate component
-    if (this.useRunestoneServies)
-        this.saveEditor();
+    if (this.useRunestoneServices) {
+        if (logFlag) {
+            this.saveEditor();
+        } else {
+            this.loadEditor().done(this.runProg.bind(this));
+        }
+    }
     this.runButton.disabled = true;
     $(this.codeDiv).addClass("ac-disabled");
 };

From 1803748687877d6044f60a4f7fcda1a5f8ae9afc Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Sun, 1 May 2016 14:43:38 -0500
Subject: [PATCH 16/21] Ensure timed is rendered after login; also fixed UL bug

---
 runestone/assess/js/timed.js     | 31 ++++++++++++++++---------------
 runestone/common/js/bookfuncs.js | 16 +++++++++-------
 2 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index 36238d6a7..980c1867b 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -181,6 +181,8 @@ Timed.prototype.renderNavControls = function () {
     // render the question number jump buttons
     this.qNumList = document.createElement("ul");
 	$(this.qNumList).attr("id", "pageNums");
+    this.qNumWrapperList = document.createElement("ul");
+    $(this.qNumWrapperList).addClass("pagination");
 	var tmpLi, tmpA;
     for (var i = 0; i < this.renderedQuestionArray.length; i++) {
 	    tmpLi = document.createElement("li");
@@ -191,18 +193,11 @@ Timed.prototype.renderNavControls = function () {
             $(tmpLi).addClass("active");
         }
         tmpLi.appendChild(tmpA);
-        this.qNumList.appendChild(tmpLi);
+        this.qNumWrapperList.appendChild(tmpLi);
     }
+    this.qNumList.appendChild(this.qNumWrapperList);
     this.navDiv.appendChild(this.qNumList);
 	this.navBtnListeners();
-
-	$(function(){
-		var tenSet = $("ul#pageNums li");
-		for (var i = 0; i < tenSet.length; i += 10) {
-			tenSet.slice(i, i + 10).wrapAll("<ul class=\"pagination\"></ul>");
-		}
-	});
-
 };
 
 Timed.prototype.navBtnListeners = function() {
@@ -493,7 +488,6 @@ Timed.prototype.tookTimedExam = function () {
         "background-color": "black",
         "color": "white"
     });
-
     var len = localStorage.length;
     if (len > 0) {
         if (localStorage.getItem(eBookConfig.email + ":" + this.divid) !== null) {
@@ -679,9 +673,16 @@ Timed.prototype.highlightNumberedList = function () {
 /*=======================================================
 === Function that calls the constructors on page load ===
 =======================================================*/
-
 $(document).ready(function () {
-    $("[data-component=timedAssessment]").each(function (index) {
-        TimedList[this.id] = new Timed({"orig": this});
-    });
-});
+    if (eBookConfig.useRunestoneServices) {
+        $(document).bind("runestone:login-complete", function () {
+            $("[data-component=timedAssessment]").each(function (index) {
+                TimedList[this.id] = new Timed({"orig": this});
+            });
+        });
+    } else {
+        $("[data-component=timedAssessment]").each(function (index) {
+            TimedList[this.id] = new Timed({"orig": this});
+        });
+    }
+})
diff --git a/runestone/common/js/bookfuncs.js b/runestone/common/js/bookfuncs.js
index add0829a9..79f8c6fc6 100644
--- a/runestone/common/js/bookfuncs.js
+++ b/runestone/common/js/bookfuncs.js
@@ -27,12 +27,12 @@
 
 //
 // Chevron functions - Must correspond with width in runestone-custom-sphinx-bootstrap.css
-// 
+//
 $(function () {
 	var resizeWindow = false;
     var	resizeWidth = 600;
 	$(window).on('resize', function (event){
-		if ($(window).width() <= resizeWidth && resizeWindow == false){ 
+		if ($(window).width() <= resizeWidth && resizeWindow == false){
 			resizeWindow = true;
 			var topPrev = $("#relations-prev").clone().attr("id", "top-relations-prev");
 			var topNext = $("#relations-next").clone().attr("id", "top-relations-next");
@@ -44,15 +44,15 @@ $(function () {
 			$("div#main-content > div").append(bottomPrev, bottomNext);
 			$("#bottom-relations-prev, #bottom-relations-next").wrapAll("<ul id=\"bottom-relations-console\"></ul>");
 		}
-		if ($(window).width() >= resizeWidth + 1 && resizeWindow == true){ 
+		if ($(window).width() >= resizeWidth + 1 && resizeWindow == true){
 			resizeWindow = false;
 			$("#top-relations-console, #bottom-relations-console").remove();
 			$("#relations-prev, #relations-next").show();
 		}
 	}).resize();
-});	
- 
- 
+});
+
+
 //
 // Logging functions
 //
@@ -134,6 +134,8 @@ function gotUser(data, status, whatever) {
         'act': 'view',
         'div_id': window.location.pathname
     })
+		// Let runestone components know they can run their javascript now
+		$(document).trigger("runestone:login-complete");
 }
 
 
@@ -301,4 +303,4 @@ $(document).ready(function() {
       e.stopPropagation();
       });
   });
-});
\ No newline at end of file
+});

From 6747522f22fe66b3ac39ed602ad7411ebecde751 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Sun, 1 May 2016 15:09:06 -0500
Subject: [PATCH 17/21] Reverting parsons

---
 runestone/parsons/css/parsons.css     |  4 --
 runestone/parsons/js/parsons_setup.js | 20 ++++-----
 runestone/parsons/js/timedparsons.js  | 63 ---------------------------
 runestone/parsons/parsons.py          |  3 +-
 4 files changed, 11 insertions(+), 79 deletions(-)
 delete mode 100644 runestone/parsons/js/timedparsons.js

diff --git a/runestone/parsons/css/parsons.css b/runestone/parsons/css/parsons.css
index 837dbd67f..7dcb5fef2 100644
--- a/runestone/parsons/css/parsons.css
+++ b/runestone/parsons/css/parsons.css
@@ -135,7 +135,3 @@ li.correctPosition, .testcase.pass {
 	margin-right: auto;
 	text-align:center;
 }
-
-.parsons-disabled {
-    pointer-events: none;
-}
diff --git a/runestone/parsons/js/parsons_setup.js b/runestone/parsons/js/parsons_setup.js
index 9be0effea..be2146a79 100644
--- a/runestone/parsons/js/parsons_setup.js
+++ b/runestone/parsons/js/parsons_setup.js
@@ -93,28 +93,28 @@ Parsons.prototype.formatCode = function () {
 == Creating/appending new HTML tags ==
 ====================================*/
 Parsons.prototype.createParsonsView = function () {         // Create DOM elements
-    this.containerDiv = document.createElement("div");
-    $(this.containerDiv).addClass("parsons alert alert-warning");
-    this.containerDiv.id = "parsons-" + this.counterId;
+    this.containingDiv = document.createElement("div");
+    $(this.containingDiv).addClass("parsons alert alert-warning");
+    this.containingDiv.id = "parsons-" + this.counterId;
 
     this.parsTextDiv = document.createElement("div");
     $(this.parsTextDiv).addClass("parsons-text");
     this.parsTextDiv.innerHTML = this.question.innerHTML;
-    this.containerDiv.appendChild(this.parsTextDiv);
+    this.containingDiv.appendChild(this.parsTextDiv);
 
     this.leftClearDiv = document.createElement("div");
     this.leftClearDiv.style["clear"] = "left";
-    this.containerDiv.appendChild(this.leftClearDiv);
+    this.containingDiv.appendChild(this.leftClearDiv);
 
     this.origDiv = document.createElement("div");
     this.origDiv.id = "parsons-orig-" + this.counterId;
     this.origDiv.style["display"] = "none";
     this.origDiv.innerHTML = this.fmtCode;
-    this.containerDiv.appendChild(this.origDiv);
+    this.containingDiv.appendChild(this.origDiv);
 
     this.sortContainerDiv = document.createElement("div");
     $(this.sortContainerDiv).addClass("sortable-code-container");
-    this.containerDiv.appendChild(this.sortContainerDiv);
+    this.containingDiv.appendChild(this.sortContainerDiv);
 
     this.sortTrashDiv = document.createElement("div");
     this.sortTrashDiv.id = "parsons-sortableTrash-" + this.counterId;
@@ -132,7 +132,7 @@ Parsons.prototype.createParsonsView = function () {         // Create DOM elemen
 
     this.parsonsControlDiv = document.createElement("div");
     $(this.parsonsControlDiv).addClass("parsons-controls");
-    this.containerDiv.appendChild(this.parsonsControlDiv);
+    this.containingDiv.appendChild(this.parsonsControlDiv);
 
     this.checkButt = document.createElement("button");
     $(this.checkButt).attr("class", "btn btn-success");
@@ -153,7 +153,7 @@ Parsons.prototype.createParsonsView = function () {         // Create DOM elemen
     this.parsonsControlDiv.appendChild(this.messageDiv);
     $(this.messageDiv).hide();
 
-    $(this.origElem).replaceWith(this.containerDiv);
+    $(this.origElem).replaceWith(this.containingDiv);
 
     this.createParsonsWidget();
 };
@@ -270,7 +270,7 @@ Parsons.prototype.tryLocalStorage = function () {
 $(document).ready(function () {
     $pjQ("[data-component=parsons]").each(function (index) {
         if ($(this.parentNode).data("component") != "timedAssessment") {
-           prsList[this.id] = new Parsons({"orig": this, "useRunestoneServices": eBookConfig.useRunestoneServices});
+           prsList[this.id] = new Parsons({"orig": this});
         }
     });
 
diff --git a/runestone/parsons/js/timedparsons.js b/runestone/parsons/js/timedparsons.js
deleted file mode 100644
index 850d40324..000000000
--- a/runestone/parsons/js/timedparsons.js
+++ /dev/null
@@ -1,63 +0,0 @@
-function TimedParsons (opts) {
-    if (opts) {
-        this.timedInit(opts);
-    }
-}
-
-TimedParsons.prototype = new Parsons();
-
-TimedParsons.prototype.timedInit = function (opts) {
-    this.init(opts);
-    this.renderTimedIcon(this.containerDiv);
-    this.hideButtons();
-};
-
-
-TimedParsons.prototype.hideButtons = function () {
-    $(this.checkButt).hide();
-};
-
-TimedParsons.prototype.renderTimedIcon = function (component) {
-    // renders the clock icon on timed components.    The component parameter
-    // is the element that the icon should be appended to.
-    var timeIconDiv = document.createElement("div");
-    var timeIcon = document.createElement("img");
-    $(timeIcon).attr({
-        "src": "../_static/clock.png",
-        "style": "width:15px;height:15px"
-    });
-    timeIconDiv.className = "timeTip";
-    timeIconDiv.title = "";
-    timeIconDiv.appendChild(timeIcon);
-    $(component).prepend(timeIconDiv);
-};
-
-TimedParsons.prototype.checkCorrectTimed = function () {
-    return this.correct ? "T" : "F";
-};
-
-TimedParsons.prototype.hideFeedback = function () {
-    $(this.messageDiv).hide();
-};
-
-TimedParsons.prototype.processTimedSubmission = function (logflag) {
-    // Disable input & evaluate component
-    var hash = this.pwidget.getHash("#ul-parsons-sortableCode-" + this.counterId);
-    if (logflag)
-        localStorage.setItem(this.divid, hash);
-    hash = this.pwidget.getHash("#ul-parsons-sortableTrash-" + this.counterId);
-    if (logflag)
-        localStorage.setItem(this.divid + "-trash", hash);
-    this.pwidget.getFeedback();
-
-    // Gross way to check if it's correct or not, but it's better than modifying the 3rd party parsons code to include a "correct" variable
-    if ($(this.messageDiv).hasClass("alert-success")) {
-        this.correct = true;
-    } else {
-        this.correct = false;
-    }
-
-    this.resetButt.disabled = true;
-    $(this.sortContainerDiv).addClass("parsons-disabled");
-
-};
diff --git a/runestone/parsons/parsons.py b/runestone/parsons/parsons.py
index 36e3fecd3..00c7dd887 100644
--- a/runestone/parsons/parsons.py
+++ b/runestone/parsons/parsons.py
@@ -37,7 +37,6 @@ def setup(app):
     app.add_javascript('parsons_setup.js')
     app.add_javascript('parsons.js')
     app.add_javascript('parsons-noconflict.js')
-    app.add_javascript('timedparsons.js')
 
 class ParsonsProblem(Assessment):
     required_arguments = 1
@@ -89,7 +88,7 @@ def findmax(alist):
         self.options['qnumber'] = self.getNumber()
         self.options['instructions'] = ""
         self.options['code'] = self.content
-
+          
         if 'maxdist' not in self.options:
             self.options['maxdist'] = '3'
         if '-----' in self.content:

From f8a39fd988effb50ce6dd02bee6337f1cd257d0f Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Sun, 1 May 2016 21:28:25 -0500
Subject: [PATCH 18/21] Missed '>>>' in merge conflict

---
 runestone/assess/js/timed.js | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index 4514a268c..ced04b253 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -633,13 +633,8 @@ Timed.prototype.restoreFromStorage = function () {
 Timed.prototype.displayScore = function () {
 
 	if (this.showResults)
-<<<<<<< HEAD
     {
        // if we have some information
-=======
-    {
-       // If we have the list of
->>>>>>> moreTimed
        if (this.correctStr.length > 0 || this.incorrectStr.length > 0 || this.skippedStr.length > 0)
        {
           var scoreString = "Num Correct: " + this.score + ". Questions: " + this.correctStr + "<br>" +

From b898a0f7cc1916f35eb8941a0a634fad27f4ebaf Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Tue, 10 May 2016 22:41:13 -0500
Subject: [PATCH 19/21] Timed parsons support minus eval re-added to PR with
 hook to be implemented

---
 runestone/parsons/css/parsons.css     |  4 ++
 runestone/parsons/js/parsons_setup.js | 26 ++++++-----
 runestone/parsons/js/timedparsons.js  | 64 +++++++++++++++++++++++++++
 runestone/parsons/parsons.py          |  3 +-
 4 files changed, 86 insertions(+), 11 deletions(-)
 create mode 100644 runestone/parsons/js/timedparsons.js

diff --git a/runestone/parsons/css/parsons.css b/runestone/parsons/css/parsons.css
index 7dcb5fef2..837dbd67f 100644
--- a/runestone/parsons/css/parsons.css
+++ b/runestone/parsons/css/parsons.css
@@ -135,3 +135,7 @@ li.correctPosition, .testcase.pass {
 	margin-right: auto;
 	text-align:center;
 }
+
+.parsons-disabled {
+    pointer-events: none;
+}
diff --git a/runestone/parsons/js/parsons_setup.js b/runestone/parsons/js/parsons_setup.js
index be2146a79..0ce3720f9 100644
--- a/runestone/parsons/js/parsons_setup.js
+++ b/runestone/parsons/js/parsons_setup.js
@@ -93,28 +93,28 @@ Parsons.prototype.formatCode = function () {
 == Creating/appending new HTML tags ==
 ====================================*/
 Parsons.prototype.createParsonsView = function () {         // Create DOM elements
-    this.containingDiv = document.createElement("div");
-    $(this.containingDiv).addClass("parsons alert alert-warning");
-    this.containingDiv.id = "parsons-" + this.counterId;
+    this.containerDiv = document.createElement("div");
+    $(this.containerDiv).addClass("parsons alert alert-warning");
+    this.containerDiv.id = "parsons-" + this.counterId;
 
     this.parsTextDiv = document.createElement("div");
     $(this.parsTextDiv).addClass("parsons-text");
     this.parsTextDiv.innerHTML = this.question.innerHTML;
-    this.containingDiv.appendChild(this.parsTextDiv);
+    this.containerDiv.appendChild(this.parsTextDiv);
 
     this.leftClearDiv = document.createElement("div");
     this.leftClearDiv.style["clear"] = "left";
-    this.containingDiv.appendChild(this.leftClearDiv);
+    this.containerDiv.appendChild(this.leftClearDiv);
 
     this.origDiv = document.createElement("div");
     this.origDiv.id = "parsons-orig-" + this.counterId;
     this.origDiv.style["display"] = "none";
     this.origDiv.innerHTML = this.fmtCode;
-    this.containingDiv.appendChild(this.origDiv);
+    this.containerDiv.appendChild(this.origDiv);
 
     this.sortContainerDiv = document.createElement("div");
     $(this.sortContainerDiv).addClass("sortable-code-container");
-    this.containingDiv.appendChild(this.sortContainerDiv);
+    this.containerDiv.appendChild(this.sortContainerDiv);
 
     this.sortTrashDiv = document.createElement("div");
     this.sortTrashDiv.id = "parsons-sortableTrash-" + this.counterId;
@@ -132,7 +132,7 @@ Parsons.prototype.createParsonsView = function () {         // Create DOM elemen
 
     this.parsonsControlDiv = document.createElement("div");
     $(this.parsonsControlDiv).addClass("parsons-controls");
-    this.containingDiv.appendChild(this.parsonsControlDiv);
+    this.containerDiv.appendChild(this.parsonsControlDiv);
 
     this.checkButt = document.createElement("button");
     $(this.checkButt).attr("class", "btn btn-success");
@@ -153,7 +153,7 @@ Parsons.prototype.createParsonsView = function () {         // Create DOM elemen
     this.parsonsControlDiv.appendChild(this.messageDiv);
     $(this.messageDiv).hide();
 
-    $(this.origElem).replaceWith(this.containingDiv);
+    $(this.origElem).replaceWith(this.containerDiv);
 
     this.createParsonsWidget();
 };
@@ -267,10 +267,16 @@ Parsons.prototype.tryLocalStorage = function () {
     }
 };
 
+// Will be implemented later to fix evaluation for parsons
+Parsons.prototype.reInitialize = function () {
+    // this.pwidget.reInitialize()
+    return null;
+};
+
 $(document).ready(function () {
     $pjQ("[data-component=parsons]").each(function (index) {
         if ($(this.parentNode).data("component") != "timedAssessment") {
-           prsList[this.id] = new Parsons({"orig": this});
+           prsList[this.id] = new Parsons({"orig": this, "useRunestoneServices": eBookConfig.useRunestoneServices});
         }
     });
 
diff --git a/runestone/parsons/js/timedparsons.js b/runestone/parsons/js/timedparsons.js
new file mode 100644
index 000000000..953279970
--- /dev/null
+++ b/runestone/parsons/js/timedparsons.js
@@ -0,0 +1,64 @@
+function TimedParsons (opts) {
+    if (opts) {
+        this.timedInit(opts);
+    }
+}
+
+TimedParsons.prototype = new Parsons();
+
+TimedParsons.prototype.timedInit = function (opts) {
+    this.init(opts);
+    this.renderTimedIcon(this.containerDiv);
+    this.hideButtons();
+};
+
+
+TimedParsons.prototype.hideButtons = function () {
+    $(this.checkButt).hide();
+};
+
+TimedParsons.prototype.renderTimedIcon = function (component) {
+    // renders the clock icon on timed components.    The component parameter
+    // is the element that the icon should be appended to.
+    var timeIconDiv = document.createElement("div");
+    var timeIcon = document.createElement("img");
+    $(timeIcon).attr({
+        "src": "../_static/clock.png",
+        "style": "width:15px;height:15px"
+    });
+    timeIconDiv.className = "timeTip";
+    timeIconDiv.title = "";
+    timeIconDiv.appendChild(timeIcon);
+    $(component).prepend(timeIconDiv);
+};
+
+TimedParsons.prototype.checkCorrectTimed = function () {
+    return this.correct ? "T" : "F";
+};
+
+TimedParsons.prototype.hideFeedback = function () {
+    $(this.messageDiv).hide();
+};
+
+TimedParsons.prototype.processTimedSubmission = function (logflag) {
+    // Disable input & evaluate component
+    this.reInitialize();
+    var hash = this.pwidget.getHash("#ul-parsons-sortableCode-" + this.counterId);
+    if (logflag)
+        localStorage.setItem(this.divid, hash);
+    hash = this.pwidget.getHash("#ul-parsons-sortableTrash-" + this.counterId);
+    if (logflag)
+        localStorage.setItem(this.divid + "-trash", hash);
+    this.pwidget.getFeedback();
+
+    // Gross way to check if it's correct or not, but it's better than modifying the 3rd party parsons code to include a "correct" variable
+    if ($(this.messageDiv).hasClass("alert-success")) {
+        this.correct = true;
+    } else {
+        this.correct = false;
+    }
+
+    this.resetButt.disabled = true;
+    $(this.sortContainerDiv).addClass("parsons-disabled");
+
+};
diff --git a/runestone/parsons/parsons.py b/runestone/parsons/parsons.py
index 145125097..de967ba2d 100644
--- a/runestone/parsons/parsons.py
+++ b/runestone/parsons/parsons.py
@@ -37,6 +37,7 @@ def setup(app):
     app.add_javascript('parsons_setup.js')
     app.add_javascript('parsons.js')
     app.add_javascript('parsons-noconflict.js')
+    app.add_javascript('timedparsons.js')
 
 class ParsonsProblem(Assessment):
     required_arguments = 1
@@ -88,7 +89,7 @@ def findmax(alist):
         self.options['qnumber'] = self.getNumber()
         self.options['instructions'] = ""
         self.options['code'] = self.content
-          
+
         if 'maxdist' not in self.options:
             self.options['maxdist'] = '5'
         if '-----' in self.content:

From 2018b703015a3668bb928cdc5bb958ac7680f09d Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Thu, 12 May 2016 18:28:03 -0500
Subject: [PATCH 20/21] Added missing login-complete triggers

---
 runestone/assess/js/timed.js     | 19 ++++++-------------
 runestone/common/js/bookfuncs.js |  8 ++++++--
 2 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/runestone/assess/js/timed.js b/runestone/assess/js/timed.js
index ced04b253..c17241b71 100644
--- a/runestone/assess/js/timed.js
+++ b/runestone/assess/js/timed.js
@@ -696,16 +696,9 @@ Timed.prototype.highlightNumberedList = function () {
 /*=======================================================
 === Function that calls the constructors on page load ===
 =======================================================*/
-$(document).ready(function () {
-    if (eBookConfig.useRunestoneServices) {
-        $(document).bind("runestone:login-complete", function () {
-            $("[data-component=timedAssessment]").each(function (index) {
-                TimedList[this.id] = new Timed({"orig": this});
-            });
-        });
-    } else {
-        $("[data-component=timedAssessment]").each(function (index) {
-            TimedList[this.id] = new Timed({"orig": this});
-        });
-    }
-})
+
+$(document).bind("runestone:login-complete", function () {
+    $("[data-component=timedAssessment]").each(function (index) {
+        TimedList[this.id] = new Timed({"orig": this});
+    });
+});
diff --git a/runestone/common/js/bookfuncs.js b/runestone/common/js/bookfuncs.js
index 79f8c6fc6..bee137d8b 100644
--- a/runestone/common/js/bookfuncs.js
+++ b/runestone/common/js/bookfuncs.js
@@ -134,8 +134,8 @@ function gotUser(data, status, whatever) {
         'act': 'view',
         'div_id': window.location.pathname
     })
-		// Let runestone components know they can run their javascript now
-		$(document).trigger("runestone:login-complete");
+	// Let runestone components know they can run their javascript now
+	$(document).trigger("runestone:login-complete");
 }
 
 
@@ -175,6 +175,8 @@ function handleLoginLogout() {
         jQuery.get(eBookConfig.ajaxURL + 'getuser', null, gotUser)
     } else {
         $(document).trigger("runestone:logout")
+		// Let runestone components know they can run their javascript now
+		$(document).trigger("runestone:login-complete");
     }
 }
 
@@ -283,6 +285,8 @@ $(document).ready(function() {
         if (typeof eBookConfig === 'undefined') {
             console.log("eBookConfig is not defined.  This page must not be set up for Runestone");
         }
+		// Let runestone components know they can run their javascript now
+		$(document).trigger("runestone:login-complete");
     }
 });
 

From 03c78614088b9783932d8ef2207d09b0544bd0d3 Mon Sep 17 00:00:00 2001
From: flysaiah <mayeis01@yahoo.com>
Date: Fri, 13 May 2016 09:53:42 -0500
Subject: [PATCH 21/21] Login-complete trigger should always happen now

---
 runestone/common/js/bookfuncs.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/runestone/common/js/bookfuncs.js b/runestone/common/js/bookfuncs.js
index bee137d8b..e4fee60d8 100644
--- a/runestone/common/js/bookfuncs.js
+++ b/runestone/common/js/bookfuncs.js
@@ -172,7 +172,7 @@ function isLoggedIn() {
 
 function handleLoginLogout() {
     if (shouldLogin()) {
-        jQuery.get(eBookConfig.ajaxURL + 'getuser', null, gotUser)
+        jQuery.get(eBookConfig.ajaxURL + 'getuser', null, gotUser).error(function () { $(document).trigger("runestone:login-complete"); });
     } else {
         $(document).trigger("runestone:logout")
 		// Let runestone components know they can run their javascript now