Added edit a gene

common/lib/capa/capa/inputtypes.py

@@ -899,3 +899,38 @@ class DesignProtein2dInput(InputTypeBase):
 
 registry.register(DesignProtein2dInput)
 
+#-----------------------------------------------------------------------------
+
+class EditAGeneInput(InputTypeBase):
+    """
+        An input type for editing a gene. Integrates with the genex java applet.
+        
+        Example:
+        
+        <editagene width="800" hight="500" dna_sequence="ETAAGGCTATAACCGA" />
+        """
+    
+    template = "editageneinput.html"
+    tags = ['editageneinput']
+    
+    @classmethod
+    def get_attributes(cls):
+        """
+            Note: width, hight, and dna_sequencee are required.
+            """
+        return [Attribute('width'),
+                Attribute('height'),
+                Attribute('dna_sequence')
+                ]
+    
+    def _extra_context(self):
+        """
+            """
+        context = {
+            'applet_loader': '/static/js/capa/edit-a-gene.js',
+        }
+        
+        return context
+
+registry.register(EditAGeneInput)
+

common/lib/capa/capa/responsetypes.py

@@ -876,7 +876,7 @@ def sympy_check2():
     allowed_inputfields = ['textline', 'textbox', 'crystallography',
                             'chemicalequationinput', 'vsepr_input',
                             'drag_and_drop_input', 'editamoleculeinput',
-                            'designprotein2dinput']
+                            'designprotein2dinput', 'editageneinput']
 
     def setup_response(self):
         xml = self.xml

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

+<section id="editageneinput_${id}" class="editageneinput">
+    <div class="script_placeholder" data-src="${applet_loader}"/>
+
+    % if status == 'unsubmitted':
+    <div class="unanswered" id="status_${id}">
+    % elif status == 'correct':
+    <div class="correct" id="status_${id}">
+    % elif status == 'incorrect':
+    <div class="incorrect" id="status_${id}">
+    % elif status == 'incomplete':
+    <div class="incorrect" id="status_${id}">
+    % endif
+
+    <object type="application/x-java-applet" id="applet_${id}" class="applet" width="${width}" height="${height}">
+      <param name="archive" value="/static/applets/capa/genex.jar" />
+      <param name="code" value="GX.GenexApplet.class" />
+      <param name="DNA_SEQUENCE" value="${dna_sequence}" />
+      Applet failed to run.  No Java plug-in was found.
+    </object>
+
+    <input type="hidden" name="input_${id}" id="input_${id}" value="${value|h}"/>
+
+    <p class="status">
+      % if status == 'unsubmitted':
+      unanswered
+      % elif status == 'correct':
+      correct
+      % elif status == 'incorrect':
+      incorrect
+      % elif status == 'incomplete':
+      incomplete
+      % endif
+    </p>
+
+    <p id="answer_${id}" class="answer"></p>
+  % if status in ['unsubmitted', 'correct', 'incorrect', 'incomplete']:
+  </div>
+% endif
+</section>

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

+(function () {
+    var timeout = 1000;
+
+    function initializeApplet(applet) {
+        console.log("Initializing " + applet);
+        waitForApplet(applet);
+    }
+
+    function waitForApplet(applet) {
+        if (applet.isActive && applet.isActive()) {
+            console.log("Applet is ready.");
+            var answerStr = applet.checkAnswer();
+            console.log(answerStr);
+            var input = $('.editageneinput input');
+            console.log(input);
+            input.val(answerStr);
+        } else if (timeout > 30 * 1000) {
+            console.error("Applet did not load on time.");
+        } else {
+            console.log("Waiting for applet...");
+            setTimeout(function() { waitForApplet(applet); }, timeout);
+        }
+    }
+    
+    var applets = $('.editageneinput object');
+    applets.each(function(i, el) { initializeApplet(el); });
+}).call(this);