Merge branch 'master' of github.com:MITx/mitx into fix/cdodge/export-draft-modules

.pylintrc

@@ -34,6 +34,7 @@ load-plugins=
 # multiple time (only on the command line, not in the configuration file where
 # it should appear only once).
 disable=
+# C0301: Line too long
 # W0141: Used builtin function 'map'
 # W0142: Used * or ** magic
 # R0201: Method could be a function
@@ -42,7 +43,7 @@ disable=
 # R0903: Too few public methods (1/2)
 # R0904: Too many public methods
 # R0913: Too many arguments
-    W0141,W0142,R0201,R0901,R0902,R0903,R0904,R0913
+    C0301,W0141,W0142,R0201,R0901,R0902,R0903,R0904,R0913
 
 
 [REPORTS]

cms/static/sass/elements/_header.scss

@@ -132,7 +132,7 @@
 
 // specific elements - course nav
 .nav-course {
-  width: 335px;
+  width: 285px;
   margin-top: -($baseline/4);
   @include font-size(14);
 

common/lib/capa/capa/inputtypes.py

@@ -1140,12 +1140,13 @@ registry.register(DesignProtein2dInput)
 
 class EditAGeneInput(InputTypeBase):
     """
-        An input type for editing a gene. Integrates with the genex java applet.
+        An input type for editing a gene.
+        Integrates with the genex GWT application.
 
         Example:
 
-        <editagene width="800" hight="500" dna_sequence="ETAAGGCTATAACCGA" />
-        """
+        <editagene genex_dna_sequence="CGAT" genex_problem_number="1"/>
+    """
 
     template = "editageneinput.html"
     tags = ['editageneinput']
@@ -1155,9 +1156,7 @@ class EditAGeneInput(InputTypeBase):
         """
         Note: width, height, and dna_sequencee are required.
         """
-        return [Attribute('width'),
-                Attribute('height'),
-                Attribute('dna_sequence'),
+        return [Attribute('genex_dna_sequence'),
                 Attribute('genex_problem_number')
                 ]
 

common/lib/capa/capa/templates/editageneinput.html

@@ -13,7 +13,7 @@
     % endif
     
     <div id="genex_container"></div>
-    <input type="hidden" name="dna_sequence" id="dna_sequence" value ="${dna_sequence}"></input>
+    <input type="hidden" name="genex_dna_sequence" id="genex_dna_sequence" value ="${genex_dna_sequence}"></input>
     <input type="hidden" name="genex_problem_number" id="genex_problem_number" value ="${genex_problem_number}"></input>
     <input type="hidden" name="input_${id}" id="input_${id}" value="${value|h}"/>
 

common/lib/xmodule/xmodule/modulestore/xml_importer.py

@@ -419,12 +419,12 @@ def remap_namespace(module, target_location_namespace):
 
     return module
 
-def validate_no_non_editable_metadata(module_store, course_id, category, allowed=[]):
+def validate_no_non_editable_metadata(module_store, course_id, category, allowed=None):
     '''
     Assert that there is no metadata within a particular category that we can't support editing
-    However we always allow display_name and 'xml_attribtues'
+    However we always allow 'display_name' and 'xml_attribtues'
     '''
-    allowed = allowed + ['xml_attributes', 'display_name']
+    _allowed = (allowed if allowed is not None else []) + ['xml_attributes', 'display_name']
 
     err_cnt = 0
     for module_loc in module_store.modules[course_id]:
@@ -432,7 +432,7 @@ def validate_no_non_editable_metadata(module_store, course_id, category, allowed
         if module.location.category == category:
             my_metadata = dict(own_metadata(module))
             for key in my_metadata.keys():
-                if key not in allowed:
+                if key not in _allowed:
                     err_cnt = err_cnt + 1
                     print ': found metadata on {0}. Studio will not support editing this piece of metadata, so it is not allowed. Metadata: {1} = {2}'. format(module.location.url(), key, my_metadata[key])
 

common/static/js/capa/edit-a-gene.js

@@ -12,22 +12,49 @@
         }
     }
     
-    //NOTE:
-    // Genex uses six global functions:
-    // genexSetDNASequence (exported from GWT)
-    // genexSetClickEvent (exported from GWT)
-    // genexSetKeyEvent (exported from GWT)
-    // genexSetProblemNumber (exported from GWT)
+    // NOTE:
+    // Genex uses 8 global functions, all prefixed with genex:
+    // 6 are exported from GWT:
+    // genexSetInitialDNASequence
+    // genexSetDNASequence
+    // genexGetDNASequence
+    // genexSetClickEvent
+    // genexSetKeyEvent
+    // genexSetProblemNumber
     //
     // It calls genexIsReady with a deferred command when it has finished 
     // initialization and has drawn itself
-    // genexStoreAnswer(answer) is called when the GWT [Store Answer] button
-    // is clicked
+    // genexStoreAnswer(answer) is called each time the DNA sequence changes
+    // through user interaction
+    
+    //Genex does not call the following function
+    genexGetInputField = function() {
+        var problem = $('#genex_container').parents('.problem');
+        return problem.find('input[type="hidden"][name!="genex_dna_sequence"][name!="genex_problem_number"]');
+    };     
     
     genexIsReady = function() {
-        //Load DNA sequence
-        var dna_sequence = $('#dna_sequence').val();
-        genexSetDNASequence(dna_sequence);
+        var input_field = genexGetInputField();
+        var genex_saved_state = input_field.val();
+        var genex_initial_dna_sequence;
+        var genex_dna_sequence;
+        
+        //Get the sequence from xml file
+        genex_initial_dna_sequence = $('#genex_dna_sequence').val();
+        //Call this function to set the value used by reset button
+        genexSetInitialDNASequence(genex_initial_dna_sequence);
+        
+        if (genex_saved_state === '') {
+            //Load DNA sequence from xml file 
+            genex_dna_sequence = genex_initial_dna_sequence;
+        }
+        else {
+            //Load DNA sequence from saved value
+            genex_saved_state = JSON.parse(genex_saved_state);
+            genex_dna_sequence = genex_saved_state.genex_dna_sequence;
+        }
+        
+        genexSetDNASequence(genex_dna_sequence);
         //Now load mouse and keyboard handlers
         genexSetClickEvent();
         genexSetKeyEvent();
@@ -35,10 +62,9 @@
         var genex_problem_number = $('#genex_problem_number').val();
         genexSetProblemNumber(genex_problem_number);    
     };
-    genexStoreAnswer = function(ans) {
-        var problem = $('#genex_container').parents('.problem');
-        var input_field = problem.find('input[type="hidden"][name!="dna_sequence"][name!="genex_problem_number"]');
-        input_field.val(ans);
+    genexStoreAnswer = function(answer) {
+        var input_field = genexGetInputField();
+        var value = {'genex_dna_sequence': genexGetDNASequence(), 'genex_answer': answer};
+        input_field.val(JSON.stringify(value));
     };
-}).call(this);
-
+}).call(this);

common/static/js/capa/genex/genex.nocache.js

@@ -1,4 +1,4 @@
-function genex(){var P='',xb='" for "gwt:onLoadErrorFn"',vb='" for "gwt:onPropertyErrorFn"',ib='"><\/script>',Z='#',Xb='.cache.html',_='/',lb='//',Qb='3F4ADBED36D589545A9300A1EA686D36',Rb='73F4B6D6D466BAD6850A60128DF5B80D',Wb=':',pb='::',dc='<script defer="defer">genex.onInjectionDone(\'genex\')<\/script>',hb='<script id="',sb='=',$='?',Sb='BA18AC23ACC5016C5D0799E864BBDFFE',ub='Bad handler "',Tb='C7B18436BA03373FB13ED589C2CCF417',cc='DOMContentLoaded',Ub='E1A9A95677AFC620CAD5759B7ACC3E67',Vb='FF175D5583BDD5ACF40C7F0AFF9A374B',jb='SCRIPT',gb='__gwt_marker_genex',kb='base',cb='baseUrl',T='begin',S='bootstrap',bb='clear.cache.gif',rb='content',Y='end',Kb='gecko',Lb='gecko1_8',Q='genex',Yb='genex.css',eb='genex.nocache.js',ob='genex::',U='gwt.codesvr=',V='gwt.hosted=',W='gwt.hybrid',wb='gwt:onLoadErrorFn',tb='gwt:onPropertyErrorFn',qb='gwt:property',bc='head',Ob='hosted.html?genex',ac='href',Jb='ie6',Ib='ie8',Hb='ie9',yb='iframe',ab='img',zb="javascript:''",Zb='link',Nb='loadExternalRefs',mb='meta',Bb='moduleRequested',X='moduleStartup',Gb='msie',nb='name',Db='opera',Ab='position:absolute;width:0;height:0;border:none',$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 genex(){var P='',xb='" for "gwt:onLoadErrorFn"',vb='" for "gwt:onPropertyErrorFn"',ib='"><\/script>',Z='#',Xb='.cache.html',_='/',lb='//',Qb='46DBCB09BEC38A6DEE76494C6517111B',Rb='557C7018CDCA52B163256408948A1722',Sb='866AF633CAA7EA4DA7E906456CDEC65A',Tb='8F9C3F1A91187AA8391FD08BA7F8716D',Wb=':',pb='::',dc='<script defer="defer">genex.onInjectionDone(\'genex\')<\/script>',hb='<script id="',sb='=',$='?',Ub='A016796CF7FB22261AE1160531B5CF82',ub='Bad handler "',cc='DOMContentLoaded',Vb='F28D6C3D881F6C18E3357AAB004477EF',jb='SCRIPT',gb='__gwt_marker_genex',kb='base',cb='baseUrl',T='begin',S='bootstrap',bb='clear.cache.gif',rb='content',Y='end',Kb='gecko',Lb='gecko1_8',Q='genex',Yb='genex.css',eb='genex.nocache.js',ob='genex::',U='gwt.codesvr=',V='gwt.hosted=',W='gwt.hybrid',wb='gwt:onLoadErrorFn',tb='gwt:onPropertyErrorFn',qb='gwt:property',bc='head',Ob='hosted.html?genex',ac='href',Jb='ie6',Ib='ie8',Hb='ie9',yb='iframe',ab='img',zb="javascript:''",Zb='link',Nb='loadExternalRefs',mb='meta',Bb='moduleRequested',X='moduleStartup',Gb='msie',nb='name',Db='opera',Ab='position:absolute;width:0;height:0;border:none',$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)}}genex=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}
@@ -13,6 +13,6 @@ function F(a){var b=u[a];return b==null?null:b}
 function G(a,b){var c=x;for(var d=0,e=a.length-1;d<e;++d){c=c[a[d]]||(c[a[d]]=[])}c[a[e]]=b}
 function H(a){var b=w[a](),c=v[a];if(b in c){return b}var d=[];for(var e in c){d[c[e]]=e}if(A){A(a,d,b)}throw null}
 var I;function J(){if(!I){I=true;var a=n.createElement(yb);a.src=zb;a.id=Q;a.style.cssText=Ab;a.tabIndex=-1;n.body.appendChild(a);o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:X,millis:(new Date).getTime(),type:Bb});a.contentWindow.location.replace(t+L)}}
-w[Cb]=function(){var b=navigator.userAgent.toLowerCase();var c=function(a){return parseInt(a[1])*1000+parseInt(a[2])};if(function(){return b.indexOf(Db)!=-1}())return Db;if(function(){return b.indexOf(Eb)!=-1}())return Fb;if(function(){return b.indexOf(Gb)!=-1&&n.documentMode>=9}())return Hb;if(function(){return b.indexOf(Gb)!=-1&&n.documentMode>=8}())return Ib;if(function(){var a=/msie ([0-9]+)\.([0-9]+)/.exec(b);if(a&&a.length==3)return c(a)>=6000}())return Jb;if(function(){return b.indexOf(Kb)!=-1}())return Lb;return Mb};v[Cb]={gecko1_8:0,ie6:1,ie8:2,ie9:3,opera:4,safari:5};genex.onScriptLoad=function(){if(I){r=true;C()}};genex.onInjectionDone=function(){q=true;o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:Nb,millis:(new Date).getTime(),type:Y});C()};E();D();var K;var L;if(B()){if(m.external&&(m.external.initModule&&m.external.initModule(Q))){m.location.reload();return}L=Ob;K=P}o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:S,millis:(new Date).getTime(),type:Pb});if(!B()){try{G([Hb],Qb);G([Fb],Rb);G([Ib],Sb);G([Lb],Tb);G([Db],Ub);G([Jb],Vb);K=x[H(Cb)];var M=K.indexOf(Wb);if(M!=-1){y=Number(K.substring(M+1));K=K.substring(0,M)}L=K+Xb}catch(a){return}}var N;function O(){if(!s){s=true;if(!__gwt_stylesLoaded[Yb]){var a=n.createElement(Zb);__gwt_stylesLoaded[Yb]=a;a.setAttribute($b,_b);a.setAttribute(ac,t+Yb);n.getElementsByTagName(bc)[0].appendChild(a)}C();if(n.removeEventListener){n.removeEventListener(cc,O,false)}if(N){clearInterval(N)}}}
+w[Cb]=function(){var b=navigator.userAgent.toLowerCase();var c=function(a){return parseInt(a[1])*1000+parseInt(a[2])};if(function(){return b.indexOf(Db)!=-1}())return Db;if(function(){return b.indexOf(Eb)!=-1}())return Fb;if(function(){return b.indexOf(Gb)!=-1&&n.documentMode>=9}())return Hb;if(function(){return b.indexOf(Gb)!=-1&&n.documentMode>=8}())return Ib;if(function(){var a=/msie ([0-9]+)\.([0-9]+)/.exec(b);if(a&&a.length==3)return c(a)>=6000}())return Jb;if(function(){return b.indexOf(Kb)!=-1}())return Lb;return Mb};v[Cb]={gecko1_8:0,ie6:1,ie8:2,ie9:3,opera:4,safari:5};genex.onScriptLoad=function(){if(I){r=true;C()}};genex.onInjectionDone=function(){q=true;o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:Nb,millis:(new Date).getTime(),type:Y});C()};E();D();var K;var L;if(B()){if(m.external&&(m.external.initModule&&m.external.initModule(Q))){m.location.reload();return}L=Ob;K=P}o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:S,millis:(new Date).getTime(),type:Pb});if(!B()){try{G([Ib],Qb);G([Fb],Rb);G([Db],Sb);G([Hb],Tb);G([Jb],Ub);G([Lb],Vb);K=x[H(Cb)];var M=K.indexOf(Wb);if(M!=-1){y=Number(K.substring(M+1));K=K.substring(0,M)}L=K+Xb}catch(a){return}}var N;function O(){if(!s){s=true;if(!__gwt_stylesLoaded[Yb]){var a=n.createElement(Zb);__gwt_stylesLoaded[Yb]=a;a.setAttribute($b,_b);a.setAttribute(ac,t+Yb);n.getElementsByTagName(bc)[0].appendChild(a)}C();if(n.removeEventListener){n.removeEventListener(cc,O,false)}if(N){clearInterval(N)}}}
 if(n.addEventListener){n.addEventListener(cc,function(){J();O()},false)}var N=setInterval(function(){if(/loaded|complete/.test(n.readyState)){J();O()}},50);o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:S,millis:(new Date).getTime(),type:Y});o&&o({moduleName:Q,sessionId:p,subSystem:R,evtGroup:Nb,millis:(new Date).getTime(),type:T});n.write(dc)}
 genex();