Merge pull request #1453 from MITx/victor/protex

Victor/protex

common/lib/capa/capa/templates/designprotein2dinput.html

 <section id="designprotein2dinput_${id}" class="designprotein2dinput">
+    <div class="script_placeholder" data-src="/static/js/capa/protex/protex.nocache.js"/>
     <div class="script_placeholder" data-src="${applet_loader}"/>
 
     % if status == 'unsubmitted':
@@ -8,16 +9,11 @@
     % elif status == 'incorrect':
     <div class="incorrect" id="status_${id}">
     % elif status == 'incomplete':
-    <div class="incorrect" id="status_${id}">
+    <div class="incomplete" id="status_${id}">
     % endif
     
-    <object type="application/x-java-applet" id="applet_${id}" class="applet" width="${width}" height="${height}">
-      <param name="archive" value="/static/applets/capa/Protex.jar" />
-      <param name="code" value="protex.ProtexApplet.class" />
-      <param name="TARGET_SHAPE" value="${target_shape}" />
-      Applet failed to run.  No Java plug-in was found.
-    </object>
-
+    <div id="protex_container"></div>
+    <input type="hidden" name="target_shape" id="target_shape" value ="${target_shape}"></input>
     <input type="hidden" name="input_${id}" id="input_${id}" value="${value|h}"/>
 
     <p class="status">

common/static/js/capa/design-protein-2d.js

 (function () {
     var timeout = 1000;
 
-    function initializeApplet(applet) {
-        console.log("Initializing " + applet);
-        waitForApplet(applet);
+    waitForProtex();
+
+    function waitForProtex() {
+        if (typeof(protex) !== "undefined" && protex) {
+            protex.onInjectionDone("protex");
+        }
+        /*if (typeof(protex) !== "undefined") {
+            //initializeProtex();    
+        }*/
+        else {
+            setTimeout(function() { waitForProtex(); }, timeout);
+        }
     }
     
-    function waitForApplet(applet) {
-        if (applet.isActive && applet.isActive()) {
-            console.log("Applet is ready.");
+    //NOTE:
+    // Protex uses three global functions:
+    // protexSetTargetShape (exported from GWT)
+    // exported protexCheckAnswer (exported from GWT)
+    // It calls protexIsReady with a deferred command when it has finished 
+    // initialization and has drawn itself
     
-            // FIXME: [rocha] This is a hack to capture the click on the check
-            // button and update the hidden field with the applet values
-            var input_field = $('.designprotein2dinput input');
+    protexIsReady = function() {
+        //Load target shape
+        var target_shape = $('#target_shape').val();
+        protexSetTargetShape(target_shape);
             
-            var problem = $(applet).parents('.problem');
+        //Get answer from protex and store it into the hidden input field
+        //when Check button is clicked
+        var problem = $('#protex_container').parents('.problem');
         var check_button = problem.find('input.check');
+        var input_field = problem.find('input[type=hidden]');
         check_button.on('click', function() {
-                var answerStr = applet.checkAnswer();
-                console.log(answerStr);
-                input_field.val(answerStr);
+            var protex_answer = protexCheckAnswer();
+            var value = {protex_answer: protex_answer};
+            input_field.val(JSON.stringify(value));
         });              
+    };
     
-        } else {
-            console.log("Waiting for applet...");
-            setTimeout(function() { waitForApplet(applet); }, timeout);
-        }
-    }
+    /*function initializeProtex() {
+        //Check to see if the two exported GWT functions protexSetTargetShape 
+        // and protexCheckAnswer have been appended to global scope -- this 
+        //happens at the end of onModuleLoad() in GWT
+        if (typeof(protexSetTargetShape) === "function" &&
+            typeof(protexCheckAnswer) === "function") {
+            
+            //Load target shape
+            var target_shape = $('#target_shape').val();
+            //protexSetTargetShape(target_shape);
             
-    var applets = $('.designprotein2dinput object');
-    applets.each(function(i, el) { initializeApplet(el); });
+            //Get answer from protex and store it into the hidden input field
+            //when Check button is clicked
+            var problem = $('#protex_container').parents('.problem');
+            var check_button = problem.find('input.check');
+        	var input_field = problem.find('input[type=hidden]');
+            check_button.on('click', function() {
+                var protex_answer = protexCheckAnswer();
+                var value = {protex_answer: protex_answer};
+                input_field.val(JSON.stringify(value));
+            });
             
+            //TO DO: Fix this, it works but is utterly ugly and unreliable
+            setTimeout(function() {
+              protexSetTargetShape(target_shape);}, 2000);
+
+        }
+        else {
+            setTimeout(function() {initializeProtex(); }, timeout);
+        }
+    }*/
 }).call(this);

common/static/js/capa/protex/hosted.html

+<html>
+<head><script>
+var $wnd = parent;
+var $doc = $wnd.document;
+var $moduleName, $moduleBase, $entry
+,$stats = $wnd.__gwtStatsEvent ? function(a) {return $wnd.__gwtStatsEvent(a);} : null
+,$sessionId = $wnd.__gwtStatsSessionId ? $wnd.__gwtStatsSessionId : null;
+// Lightweight metrics
+if ($stats) {
+  var moduleFuncName = location.search.substr(1);
+  var moduleFunc = $wnd[moduleFuncName];
+  var moduleName = moduleFunc ? moduleFunc.moduleName : "unknown";
+  $stats({moduleName:moduleName,sessionId:$sessionId,subSystem:'startup',evtGroup:'moduleStartup',millis:(new Date()).getTime(),type:'moduleEvalStart'});
+}
+var $hostedHtmlVersion="2.1";
+
+var gwtOnLoad;
+var $hosted = "localhost:9997";
+
+function loadIframe(url) {
+  var topDoc = window.top.document;
+
+  // create an iframe
+  var iframeDiv = topDoc.createElement("div");
+  iframeDiv.innerHTML = "<iframe scrolling=no frameborder=0 src='" + url + "'>";
+  var iframe = iframeDiv.firstChild;
+  
+  // mess with the iframe style a little
+  var iframeStyle = iframe.style;
+  iframeStyle.position = "absolute";
+  iframeStyle.borderWidth = "0";
+  iframeStyle.left = "0";
+  iframeStyle.top = "0";
+  iframeStyle.width = "100%";
+  iframeStyle.backgroundColor = "#ffffff";
+  iframeStyle.zIndex = "1";
+  iframeStyle.height = "100%";
+
+  // update the top window's document's body's style
+  var hostBodyStyle = window.top.document.body.style; 
+  hostBodyStyle.margin = "0";
+  hostBodyStyle.height = iframeStyle.height;
+  hostBodyStyle.overflow = "hidden";
+
+  // insert the iframe
+  topDoc.body.insertBefore(iframe, topDoc.body.firstChild);
+}
+
+var ua = navigator.userAgent.toLowerCase();
+if (ua.indexOf("gecko") != -1) {
+  // install eval wrapper on FF to avoid EvalError problem
+  var __eval = window.eval;
+  window.eval = function(s) {
+    return __eval(s);
+  }
+}
+if (ua.indexOf("chrome") != -1) {
+  // work around __gwt_ObjectId appearing in JS objects
+  var hop = Object.prototype.hasOwnProperty;
+  Object.prototype.hasOwnProperty = function(prop) {
+    return prop != "__gwt_ObjectId" && hop.call(this, prop);
+  };
+  // do the same in our parent as well -- see issue 4486
+  // NOTE: this will have to be changed when we support non-iframe-based DevMode 
+  var hop2 = parent.Object.prototype.hasOwnProperty;
+  parent.Object.prototype.hasOwnProperty = function(prop) {
+    return prop != "__gwt_ObjectId" && hop2.call(this, prop);
+  };
+}
+
+// wrapper to call JS methods, which we need both to be able to supply a
+// different this for method lookup and to get the exception back
+function __gwt_jsInvoke(thisObj, methodName) {
+  try {
+    var args = Array.prototype.slice.call(arguments, 2);
+    return [0, window[methodName].apply(thisObj, args)];
+  } catch (e) {
+    return [1, e];
+  }
+}
+
+var __gwt_javaInvokes = [];
+function __gwt_makeJavaInvoke(argCount) {
+  return __gwt_javaInvokes[argCount] || __gwt_doMakeJavaInvoke(argCount);
+}
+
+function __gwt_doMakeJavaInvoke(argCount) {
+  // IE6 won't eval() anonymous functions except as r-values
+  var argList = "";
+  for (var i = 0; i < argCount; i++) {
+    argList += ",p" + i;
+  }
+  var argListNoComma = argList.substring(1);
+
+  return eval(
+    "__gwt_javaInvokes[" + argCount + "] =\n" +
+    "  function(thisObj, dispId" + argList + ") {\n" +
+    "    var result = __static(dispId, thisObj" + argList + ");\n" +
+    "    if (result[0]) {\n" +
+    "      throw result[1];\n" +
+    "    } else {\n" +
+    "      return result[1];\n" +
+    "    }\n" +
+    "  }\n"
+  ); 
+}
+
+/*
+ * This is used to create tear-offs of Java methods.  Each function corresponds
+ * to exactly one dispId, and also embeds the argument count.  We get the "this"
+ * value from the context in which the function is being executed.
+ * Function-object identity is preserved by caching in a sparse array.
+ */
+var __gwt_tearOffs = [];
+var __gwt_tearOffGenerators = [];
+function __gwt_makeTearOff(proxy, dispId, argCount) {
+  return __gwt_tearOffs[dispId] || __gwt_doMakeTearOff(dispId, argCount);
+}
+
+function __gwt_doMakeTearOff(dispId, argCount) {
+  return __gwt_tearOffs[dispId] = 
+      (__gwt_tearOffGenerators[argCount] || __gwt_doMakeTearOffGenerator(argCount))(dispId);
+}
+
+function __gwt_doMakeTearOffGenerator(argCount) {
+  // IE6 won't eval() anonymous functions except as r-values
+  var argList = "";
+  for (var i = 0; i < argCount; i++) {
+    argList += ",p" + i;
+  }
+  var argListNoComma = argList.substring(1);
+
+  return eval(
+    "__gwt_tearOffGenerators[" + argCount + "] =\n" +
+    "  function(dispId) {\n" +
+    "    return function(" + argListNoComma + ") {\n" +
+    "      var result = __static(dispId, this" + argList + ");\n" +
+    "      if (result[0]) {\n" +
+    "        throw result[1];\n" +
+    "      } else {\n" +
+    "        return result[1];\n" +
+    "      }\n" +
+    "    }\n" +
+    "  }\n"
+  ); 
+}
+
+function __gwt_makeResult(isException, result) {
+  return [isException, result];
+}
+
+function __gwt_disconnected() {
+  // Prevent double-invocation.
+  window.__gwt_disconnected = new Function();
+  // Do it in a timeout so we can be sure we have a clean stack.
+  window.setTimeout(__gwt_disconnected_impl, 1);
+}
+
+function __gwt_disconnected_impl() {
+  __gwt_displayGlassMessage('GWT Code Server Disconnected',
+      'Most likely, you closed GWT Development Mode. Or, you might have lost '
+      + 'network connectivity. To fix this, try restarting GWT Development Mode and '
+      + 'refresh this page.');
+}
+
+// Keep track of z-index to allow layering of multiple glass messages
+var __gwt_glassMessageZIndex = 2147483647;
+
+// Note this method is also used by ModuleSpace.java
+function __gwt_displayGlassMessage(summary, details) {
+  var topWin = window.top;
+  var topDoc = topWin.document;
+  var outer = topDoc.createElement("div");
+  // Do not insert whitespace or outer.firstChild will get a text node.
+  outer.innerHTML = 
+    '<div style="position:absolute;z-index:' + __gwt_glassMessageZIndex-- +
+    ';left:50px;top:50px;width:600px;color:#FFF;font-family:verdana;text-align:left;">' +
+    '<div style="font-size:30px;font-weight:bold;">' + summary + '</div>' +
+    '<div style="font-size:15px;">' + details + '</div>' +
+    '</div>' +
+    '<div style="position:absolute;z-index:' + __gwt_glassMessageZIndex-- +
+    ';left:0px;top:0px;right:0px;bottom:0px;filter:alpha(opacity=60);opacity:0.6;background-color:#000;"></div>'
+  ;
+  topDoc.body.appendChild(outer);
+  var glass = outer.firstChild;
+  var glassStyle = glass.style;
+
+  // Scroll to the top and remove scrollbars.
+  topWin.scrollTo(0, 0);
+  if (topDoc.compatMode == "BackCompat") {
+    topDoc.body.style["overflow"] = "hidden";
+  } else {
+    topDoc.documentElement.style["overflow"] = "hidden";
+  }
+
+  // Steal focus.
+  glass.focus();
+
+  if ((navigator.userAgent.indexOf("MSIE") >= 0) && (topDoc.compatMode == "BackCompat")) {
+    // IE quirks mode doesn't support right/bottom, but does support this.
+    glassStyle.width = "125%";
+    glassStyle.height = "100%";
+  } else if (navigator.userAgent.indexOf("MSIE 6") >= 0) {
+    // IE6 doesn't have a real standards mode, so we have to use hacks.
+    glassStyle.width = "125%"; // Get past scroll bar area.
+    // Nasty CSS; onresize would be better but the outer window won't let us add a listener IE.
+    glassStyle.setExpression("height", "document.documentElement.clientHeight");
+  }
+
+  $doc.title = summary + " [" + $doc.title + "]";
+}
+
+function findPluginObject() {
+  try {
+    return document.getElementById('pluginObject');
+  } catch (e) {
+    return null;
+  }
+}
+
+function findPluginEmbed() {
+  try {
+    return document.getElementById('pluginEmbed')
+  } catch (e) {
+    return null;
+  }
+}
+
+function findPluginXPCOM() {
+  try {
+    return __gwt_HostedModePlugin;
+  } catch (e) {
+    return null;
+  }
+}
+
+gwtOnLoad = function(errFn, modName, modBase){
+  $moduleName = modName;
+  $moduleBase = modBase;
+
+  // Note that the order is important
+  var pluginFinders = [
+    findPluginXPCOM,
+    findPluginObject,
+    findPluginEmbed,
+  ];
+  var topWin = window.top;
+  var url = topWin.location.href;
+  if (!topWin.__gwt_SessionID) {
+    var ASCII_EXCLAMATION = 33;
+    var ASCII_TILDE = 126;
+    var chars = [];
+    for (var i = 0; i < 16; ++i) {
+      chars.push(Math.floor(ASCII_EXCLAMATION
+          + Math.random() * (ASCII_TILDE - ASCII_EXCLAMATION + 1)));
+    }
+    topWin.__gwt_SessionID = String.fromCharCode.apply(null, chars);
+  }
+  var plugin = null;
+  for (var i = 0; i < pluginFinders.length; ++i) {
+    try {
+      var maybePlugin = pluginFinders[i]();
+      if (maybePlugin != null && maybePlugin.init(window)) {
+        plugin = maybePlugin;
+        break;
+      }
+    } catch (e) {
+    }
+  }
+  if (!plugin) {
+    // try searching for a v1 plugin for backwards compatibility
+    var found = false;
+    for (var i = 0; i < pluginFinders.length; ++i) {
+      try {
+        plugin = pluginFinders[i]();
+        if (plugin != null && plugin.connect($hosted, $moduleName, window)) {
+          return;
+        }
+      } catch (e) {
+      }
+    }
+    loadIframe("http://gwt.google.com/missing-plugin");
+  } else {
+    if (plugin.connect(url, topWin.__gwt_SessionID, $hosted, $moduleName,
+        $hostedHtmlVersion)) {
+      window.onUnload = function() {
+        try {
+          // wrap in try/catch since plugins are not required to supply this
+          plugin.disconnect();
+        } catch (e) {
+        }
+      };
+    } else {
+      if (errFn) {
+        errFn(modName);
+      } else {
+        __gwt_displayGlassMessage(
+            "Plugin failed to connect to Development Mode server at " + simpleEscape($hosted),
+            "Follow the troubleshooting instructions at "
+            + "<a href='http://code.google.com/p/google-web-toolkit/wiki/TroubleshootingOOPHM'>"
+            + "http://code.google.com/p/google-web-toolkit/wiki/TroubleshootingOOPHM</a>");
+      }
+    }
+  }
+}
+
+function simpleEscape(originalString) {
+  return originalString.replace(/&/g,"&amp;")
+    .replace(/</g,"&lt;")
+    .replace(/>/g,"&gt;")
+    .replace(/\'/g, "&#39;")
+    .replace(/\"/g,"&quot;");
+}
+
+window.onunload = function() {
+};
+
+// Lightweight metrics
+window.fireOnModuleLoadStart = function(className) {
+  $stats && $stats({moduleName:$moduleName, sessionId:$sessionId, subSystem:'startup', evtGroup:'moduleStartup', millis:(new Date()).getTime(), type:'onModuleLoadStart', className:className});
+};
+
+window.__gwt_module_id = 0;
+</script></head>
+<body>
+<font face='arial' size='-1'>This html file is for Development Mode support.</font>
+<script><!--
+// Lightweight metrics
+$stats && $stats({moduleName:$moduleName, sessionId:$sessionId, subSystem:'startup', evtGroup:'moduleStartup', millis:(new Date()).getTime(), type:'moduleEvalEnd'});
+
+// OOPHM currently only supports IFrameLinker
+var query = parent.location.search;
+if (!findPluginXPCOM()) {
+  document.write('<embed id="pluginEmbed" type="application/x-gwt-hosted-mode" width="10" height="10">');
+  document.write('</embed>');
+  document.write('<object id="pluginObject" CLASSID="CLSID:1D6156B6-002B-49E7-B5CA-C138FB843B4E">');
+  document.write('</object>');
+}
+
+// look for the old query parameter if we don't find the new one
+var idx = query.indexOf("gwt.codesvr=");
+if (idx >= 0) {
+  idx += 12;  // "gwt.codesvr=".length() == 12
+} else {
+  idx = query.indexOf("gwt.hosted=");
+  if (idx >= 0) {
+    idx += 11;  // "gwt.hosted=".length() == 11
+  }
+}
+if (idx >= 0) {
+  var amp = query.indexOf("&", idx);
+  if (amp >= 0) {
+    $hosted = query.substring(idx, amp);
+  } else {
+    $hosted = query.substring(idx);
+  }
+
+  // According to RFC 3986, some of this component's characters (e.g., ':')
+  // are reserved and *may* be escaped.
+  $hosted = decodeURIComponent($hosted);
+}
+
+query = window.location.search.substring(1);
+if (query && $wnd[query]) setTimeout($wnd[query].onScriptLoad, 1);
+--></script></body></html>

common/static/js/capa/protex/protex.css

+.protex-absolute-panel {
+   background-color: #BBBBBB;
+}
+
+.protex-canvas {
+	outline: none;
+}
+
+.protex-caption-panel {
+	padding: 10px 10px 10px 10px;
+	margin: 0px 0px 0px 0px;
+	border:2px solid #4E4E4E;
+    font: normal normal normal 14pt/normal 'Open Sans', sans-serif;
+	background-color: #B2B2FF;
+}
+
+.protex-textbox {
+    font: normal normal normal 12pt/normal 'Open Sans', sans-serif !important;
+    padding: 2px 2px 2px 2px !important;
+}
+
+.protex-caption-panel-ss-bonds-on {
+    padding: 10px 10px 10px 10px;
+	margin: 0px 0px 0px 0px;
+	border:2px solid #4E4E4E;
+    font: normal normal normal 14pt/normal 'Open Sans', sans-serif;
+	background-color: #B2FFFF;	
+}
+
+.protex-button {
+    margin-right: 15px;
+}
+
+.protex-listbox {
+}
+
+.gwt-ProgressBar-shell {
+  border: 2px solid #faf9f7;
+  border-right: 2px solid #848280;
+  border-bottom: 2px solid #848280;
+  background-color: #AAAAAA;
+  height: 14pt;
+  width: 50%;
+  margin-left: 15px;
+}
+.gwt-ProgressBar-shell .gwt-ProgressBar-bar {
+  background-color: #67A7E3;
+}
+.gwt-ProgressBar-shell .gwt-ProgressBar-text {
+  padding: 0px;
+  margin: 0px;
+  color: white;
+}

common/static/js/capa/protex/protex.nocache.js

+function protex(){var P='',xb='" for "gwt:onLoadErrorFn"',vb='" for "gwt:onPropertyErrorFn"',ib='"><\/script>',Z='#',Xb='.cache.html',_='/',lb='//',Qb='39CC89519B0E1FCB47B935AC9FE13D7B',Rb='6E05B1CD5BFCAF7D53C7C64D84318178',Wb=':',pb='::',dc='<script defer="defer">protex.onInjectionDone(\'protex\')<\/script>',hb='<script id="',sb='=',$='?',ub='Bad handler "',Sb='C824A958AB642DC2213DFFDAC640BEAA',Tb='D9267DE8FB02F8B995B4A58C66C76E29',cc='DOMContentLoaded',Ub='F275492F7098103BCB05F4F86ABF6218',Vb='F3301B0E65F38C7FCF2EF3764B3BB0B6',jb='SCRIPT',gb='__gwt_marker_protex',kb='base',cb='baseUrl',T='begin',S='bootstrap',bb='clear.cache.gif',rb='content',Y='end',Kb='gecko',Lb='gecko1_8',U='gwt.codesvr=',V='gwt.hosted=',W='gwt.hybrid',wb='gwt:onLoadErrorFn',tb='gwt:onPropertyErrorFn',qb='gwt:property',bc='head',Ob='hosted.html?protex',ac='href',Jb='ie6',Ib='ie8',Hb='ie9',yb='iframe',ab='img',zb="javascript:''",Zb='link',Nb='loadExternalRefs',mb='meta',Bb='moduleRequested',X='moduleStartup',Gb='msie',nb='name',Db='opera',Ab='position:absolute;width:0;height:0;border:none',Q='protex',Yb='protex.css',eb='protex.nocache.js',ob='protex::',$b='rel',Fb='safari',db='script',Pb='selectingPermutation',R='startup',_b='stylesheet',fb='undefined',Mb='unknown',Cb='user.agent',Eb='webkit';var m=window,n=document,o=m.__gwtStatsEvent?function(a){return m.__gwtStatsEvent(a)}:null,p=m.__gwtStatsSessionId?m.__gwtStatsSessionId:null,q,r,s,t=P,u={},v=[],w=[],x=[],y=0,z,A;o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:S,millis:(new Date).getTime(),type:T});if(!m.__gwt_stylesLoaded){m.__gwt_stylesLoaded={}}if(!m.__gwt_scriptsLoaded){m.__gwt_scriptsLoaded={}}function B(){var b=false;try{var c=m.location.search;return (c.indexOf(U)!=-1||(c.indexOf(V)!=-1||m.external&&m.external.gwtOnLoad))&&c.indexOf(W)==-1}catch(a){}B=function(){return b};return b}
+function C(){if(q&&r){var b=n.getElementById(Q);var c=b.contentWindow;if(B()){c.__gwt_getProperty=function(a){return H(a)}}protex=null;c.gwtOnLoad(z,Q,t,y);o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:X,millis:(new Date).getTime(),type:Y})}}
+function D(){function e(a){var b=a.lastIndexOf(Z);if(b==-1){b=a.length}var c=a.indexOf($);if(c==-1){c=a.length}var d=a.lastIndexOf(_,Math.min(c,b));return d>=0?a.substring(0,d+1):P}
+function f(a){if(a.match(/^\w+:\/\//)){}else{var b=n.createElement(ab);b.src=a+bb;a=e(b.src)}return a}
+function g(){var a=F(cb);if(a!=null){return a}return P}
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