diff --git a/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_QryTool.js b/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_QryTool.js
index c50bc9266..fac996c08 100644
--- a/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_QryTool.js
+++ b/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_QryTool.js
@@ -1,775 +1,784 @@
 i2b2.MedCo.QT = {};
 
 var pieResultParam = {
     "header": {
         "title": {
             "font": "cinzel",
             "text": "#patients",
             "color": "#000000",
             "fontSize": 24
         },
         "location": "pie-center",
     },
 
     "size": {
         "canvasHeight": 400,
         "canvasWidth": 600,
         "pieInnerRadius": "59%",
         "pieOuterRadius": "63%"
     },
 
     "data": {
         "sortOrder": "label-desc",
         "content": {}
     },
 
     "labels": {
         "outer": {
             "format": "label-value2",
             "pieDistance": 20
         },
         "inner": {
             "format": "none"
         },
         "mainLabel": {
             "font": "cinzel",
             "fontSize": 15
         },
         "percentage": {
             "font": "cinzel",
             "color": "#999999",
             "fontSize": 8,
             "decimalPlaces": 0
         },
         "value": {
             "font": "cinzel",
             "color": "#000000",
             "fontSize": 15,
             "fontWeight": 600
         },
         "lines": {
             "enabled": true,
         },
         "truncation": {
             "enabled": true
         }
     },
 
     "tooltips": {
         "enabled": true,
         "type": "placeholder",
         "string": "{label}: {value}, {percentage}%",
         "styles": {
             "fontSize": 15,
             "backgroundOpacity": 0.70,
             "borderRadius": 15,
             "padding": 7
         }
     },
     "effects": {
         "load": {
             "speed": 500
         },
         "pullOutSegmentOnClick": {
             "effect": "none",
         },
         "highlightLuminosity": 0.3
     },
 
     "misc": {
         "colors": {
             "segmentStroke": "#000000"
         },
         "pieCenterOffset": {
             "y": -50
         }
     }
 }
 var currId = 0; // used to give a unique id to the panels
 
 function getPanelIndex(panel){
     while (panel.className != 'MedCo-QueryPanel'){
         if (!panel.parentElement){
             return -1
         }
         panel = panel.parentElement
     }
     var index = Array.prototype.indexOf.call(panel.parentNode.children, panel);
     return index
 }
 
 function htmlToElement(html) {
     var template = document.createElement('template');
     html = html.trim(); // Never return a text node of whitespace as the result
     template.innerHTML = html;
     return template.content.firstChild;
 }
 
 
 i2b2.MedCo.QT.ctrlr = {};
 
 i2b2.MedCo.QT.ctrlr.init = function(){
     // Initialization of the query tool.
 
     var num_panels = 3; // start with 3 panels
 
     i2b2.MedCo.QT.panels = [];
 
     for (var i=0; i < num_panels; i++) {
         i2b2.MedCo.QT.ctrlr.appendPanel()
     }
 
     // i2b2.MedCo.QT.query.init();
 };
 
 i2b2.MedCo.QT.ctrlr.clear = function (){
     // todo and ignore a possible query result?
     // clear all the panels
     var panels = i2b2.MedCo.QT.panels;
     for(var i = 0; i < panels.length; i++){
         panels[i].ctrlr.clear()
     }
 };
 
 i2b2.MedCo.QT.timer = {
     // number of milliseconds between two updates
     step: 100,
 
     // store the start time (in milliseconds)
     startTime: 0,
 
     //store the pointer to the interval object so to stop it
     timeinterval: null,
 
     start: function () {
         // hide the gif and start
         document.getElementById("medcoTimer").style.display = 'inline-block';
         document.getElementById("MedCo-loadingGif").style.display = 'none';
 
         var context = i2b2.MedCo.QT.timer;
         context.clear();
         context.startTime = new Date().getTime();
         context.timeinterval = setInterval(context.update, context.step);
     },
 
     update: function () {
         var now = new Date().getTime();
         document.querySelector("#medcoTimer").innerHTML = ((now-i2b2.MedCo.QT.timer.startTime)/1000).toFixed(2);
     },
 
     stop: function () {
         clearInterval(i2b2.MedCo.QT.timer.timeinterval);
         i2b2.MedCo.QT.timer.timeinterval = null;
     },
 
     clear: function(){
         i2b2.MedCo.QT.timer.stop();
         document.querySelector("#medcoTimer").innerHTML = 0;
     },
 
     wait: function(){
         // show the gif
         document.getElementById("medcoTimer").style.display = 'none';
         document.getElementById("MedCo-loadingGif").style.display = 'inline';
     }
 };
 
 
 i2b2.MedCo.QT.query = {
     // timeout used to wait until we received all the variant ids
     timeout: null,
 
     // You should call this function to run a query so to make sure you received and encrypted all
     // the annotation ids you queried
     waitThenRun: function(qryName, qryType){
         // - qryName: name of the query
         // - qryType: query type. Must be a string in {"PATIENT_COUNT_XML", "PATIENTSET"}
         // - budget: selected budget // todo delete (not used), or add obfuscated query count
         // alert(qryName + " " + qryType);
         // return; // todo delete
 
         // clear any previous timeout (in case the user keeps pressing "run query" we want to send only one query)
         clearTimeout(i2b2.MedCo.QT.query.timeout);
 
         // clear the timer in any case
         i2b2.MedCo.QT.timer.clear();
         // show that we are preparing to send the query
         i2b2.MedCo.QT.timer.wait();
 
         // wait until you receive all the variants you requested and all of them have been encrypted
         if (i2b2.MedCo.ctrlr.pendingVariantsQueries != 0 || !i2b2.MedCo.ctrlr.background.encryptionDone()) { // todo change names
             // try again later to run the query
             i2b2.MedCo.QT.query.timeout = setTimeout(i2b2.MedCo.QT.query.waitThenRun, 500);
             return
         }
 
         // the query can be build and sent
         i2b2.MedCo.QT.query.run(qryName, qryType);
     },
 
     // build and send the query
     run: function(qryName, qryType){
         // start the timer
         i2b2.MedCo.QT.timer.start();
 
         // callback processor to run the query from definition
         this.MedCocallback = new i2b2_scopedCallback();
         this.MedCocallback.scope = this;
         this.MedCocallback.callback = function(results) {
             // //		"results" object contains the following attributes:
             // //			refXML: xmlDomObject <--- for data processing
             // //			msgRequest: xml (string)
             // //			msgResponse: xml (string)
             // //			error: boolean
             // //			errorStatus: string [only with error=true]
             // //			errorMsg: string [only with error=true]
 
             // stop the timer and the gif
             i2b2.MedCo.QT.timer.stop();
 
             try{
                 if (results.error) {
                     alert(results.errorMsg);
                     return;
                 } else {
                     // extract and show the patient counts
                     i2b2.MedCo.QT.query.showResponse(results, "MedCo-QueryResults");
                 }
             } catch(e){
                 alert("Error when extracting the results of the query: " + e.message)
             }
         };
 
         // <result_output_list>
         //     <result_output name="PATIENT_COUNT_XML"/>
         //     <result_output name="PATIENTSET"/>
         // </result_output_list>
 
         // todo: delete. Shrine changes <result_output_list> and many other field setting them with default values
         // for testing we decided to put the query type in the query name field and parse it on the server side
         qryName += "|" + qryType;
 
         this.MedCoparams = {};
         this.MedCoparams.psm_query_definition = i2b2.MedCo.QT.query.buildQueryDefinition(qryName);
         this.MedCoparams.psm_result_output = "<result_output_list>\n\t\t<result_output priority_index='9' name='" + qryType + "'/>\n\t</result_output_list>";
         // this.MedCoparams.psm_result_output = "<result_output_list><result_output priority_index='9' name='patient_count_xml'/>\n</result_output_list>\n";
 
         i2b2.CRC.ajax.runQueryInstance_fromQueryDefinition("PLUGIN:MedCo", this.MedCoparams, this.MedCocallback);
     },
 
     showResponse: function(response, resultDiv){
         // The response fo each Hospital is expected to contain:
         // - result_type: indicates the type of result, is either one of
         //          "agg_result": each hospital returned the whole encrypted count
         //          "total": each hospital returned its encrypted count
         //          "patient_set": each hospital returned its set of patients
         // - result: the corresponding result
         // note: the result_type field is the same for every hospital
 
         response = response.refXML.getElementsByTagName('query_result_instance');
 
         // first extract the results
         var institutions = new Array(response.length);
         var result_type;
         for (var i = 0; i < response.length; i++) {
             try {
                 var currInstitution = JSON.parse(i2b2.h.getXNodeVal(response[i], 'description'));
                 var instName = Object.keys(currInstitution)[0];
 
                 result_type = currInstitution[instName]["result_type"]
 
                 institutions[i] = {
                     label: instName,
                     result: currInstitution[instName]["result"],
                 };
 
                 if (result_type == "agg_result" || result_type == "total") {
                     // agg_result and total indicates the the presence of an encrypted result
                     i2b2.MedCo.ctrlr.background.toBeDecrypted([institutions[i].result]);
                 }
 
                 if (result_type == "total"){
                     // If the query type is "total" then the three hospitals returned three equal values
                     // break; // todo
                 }
             } catch (e) {
                 alert("Error in extracting the response." + i2b2.h.getXNodeVal(response[i], 'summary'));
                 return
             }
         }
 
         // todo show properly the different results
         var resultPanel = document.getElementById(resultDiv)
         while (resultPanel.firstChild) {
             resultPanel.removeChild(resultPanel.firstChild);
         }
         switch(result_type) {
             case "agg_result":
                 // wait until all ciphertexts are decrypted and show the pie
                 var checkThenShow = function(){
                     if (i2b2.MedCo.ctrlr.background.decryptionDone()) {
                         var totPatientCount = 0;
                         for (var i = 0; i < institutions.length; i++){
                             institutions[i].value = i2b2.MedCo.ctrlr.background.decryptionCache[institutions[i].result];
                             totPatientCount += institutions[i].value;
                         }
 
                         // if there are no patients that match the query then do not display the pie chart
                         if (totPatientCount == 0) {
                             resultPanel.innerHTML = "No patient matches the query";
                             return
                         }
 
                         pieResultParam.data.content = institutions;
                         new d3pie(resultDiv, pieResultParam);
                     }
                     else{
                         setTimeout(checkThenShow, 100)
                     }
                 };
 
                 checkThenShow();
                 break;
             case "total":
                 // wait fot all the ciphertext to get decrypted and show the total number of patients
                 var checkThenShow = function(){
                     if (i2b2.MedCo.ctrlr.background.decryptionDone()) {
                         var totPatientCount = i2b2.MedCo.ctrlr.background.decryptionCache[institutions[0].result];
 
                         document.getElementById(resultDiv).appendChild(htmlToElement(
                             "<table class=\"MedCo-TotalResult\">" +
                                 "<tbody>" +
                                     "<tr><td></td></tr>" +
                                     "<tr class=\"small-row\"><td>Number of patients</td></tr>"+
                                     "<tr class=\"count_row\">" +
                                         "<td>" +
                                         totPatientCount +
                                         "</td>"+
                                     "</tr>"+
                                     "<tr class=\"small-row\">" +
                                         "<td>" +
                                         // "For Query mild dementia@10:21:25" +
                                         "</td>" +
                                     "</tr>" +
                                     "<tr><td></td></tr>" +
                                 "</tbody>" +
                             "</table>"
                         )
                     )
                     }
                     else{
                         setTimeout(checkThenShow, 100)
                     }
                 };
                 checkThenShow();
                 break;
             case "patient_set":
                 var res = document.getElementById(resultDiv);
                 res.innerHTML = "";
 
                 for (var i = 0; i < institutions.length; i++){
                     institutions[i].value = i2b2.MedCo.ctrlr.background.decryptionCache[institutions[i].result];
                     res.innerHTML += institutions[i].label + ": " + institutions[i].result + "<br>"
                 }
 
                 break;
         }
 
 
 
     },
 
     defaultQryName: function(){
         var d = new Date();
         var time =
             d.getHours().toString() + ":" +
             d.getMinutes().toString() + ":" +
             d.getSeconds().toString();
         //  + ":" + d.getMilliseconds().toString();
         return "MedCo_query" + "@" + time;
     },
 
     // build the xml of the query from i2b2.MedCo.QT.panels
     buildQueryDefinition: function(qryName){
         // name: name for the query
 
         // get the time of the query (we concatenate the time to the name of the query)
         // var d = new Date();
         // var time =
         //     d.getHours().toString() + ":" +
         //     d.getMinutes().toString() + ":" +
         //     d.getSeconds().toString() + ":" +
         //     d.getMilliseconds().toString();
         // var rand = Math.random()+""
         var queryxml = "<query_definition>\n\t<query_name>" + qryName + "</query_name>\n\t<query_timing>ANY</query_timing>\n\t<specificity_scale>0</specificity_scale>";
 
         var panels = i2b2.MedCo.QT.panels;
         for (var i = 0 ; i < panels.length; i++){ // there are 3 panels
             if (panels[i].ctrlr.isEmpty()) {continue} // if in the panel there are no parameters the go to the next panel
 
             // open a panel object in which we put all its concepts
             queryxml +=
                 "\n\t<panel>\n\t\t" +
                 "<panel_number>" + i + "</panel_number>\n\t\t" +
                 "<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t" +
                 "<invert>" + (panels[i].model.exclude ? 1 : 0) + "</invert>\n\t\t" +
                 "<panel_timing>ANY</panel_timing>\n\t\t" +
                 "<total_item_occurrences>1</total_item_occurrences>\n\t\t";
 
             // put the all the concepts in the query
             for (var j = 0; j < panels[i].model.content.length; j++){
                 // take one "row" at a time and take encrypted values if sensitive
                 var item_keys = [];
                 var row = panels[i].model.content[j];
                 var dateConstraint = panels[i].model.date.model;
 
                 if (row.sensitive){
                     // the row contains sensitive values
                     for (var z=0; z<row.values.length; z++) {
-                        item_keys.push("\\\\ENCRYPTED_KEY\\" + i2b2.MedCo.ctrlr.background.encryptionCache[row.values[z]] + "\\")
+                        var key = "";
+                        if (row.already_encrypted) {
+                            key = row.values[z]
+                        }
+                        else{
+                            key = i2b2.MedCo.ctrlr.background.encryptionCache[row.values[z]]
+                        }
+                        item_keys.push("\\\\ENCRYPTED_KEY\\" +  + "\\")
                     }
                 }
                 else{
                     item_keys = row.values
                 }
 
                 for (var z=0; z<item_keys.length; z++) {
                     queryxml +=
                         "<item>\n\t\t\t" +
                             "<item_key>" + item_keys[z] + "</item_key>\n\t\t"
 
                     if (dateConstraint.dateFrom || dateConstraint.dateTo){
                         queryxml +=
                             "\t<constrain_by_date>" +
                                 (dateConstraint.dateFrom ? "\n\t\t\t\t<date_from>" + dateConstraint.dateFrom.Year + "-" + dateConstraint.dateFrom.Month + "-" + dateConstraint.dateFrom.Day + "T00:00:00.000-05:00'</date_from>\n\t\t\t" : "") +
                                 (dateConstraint.dateTo ? "\n\t\t\t\t<date_to>" + dateConstraint.dateTo.Year + "-" + dateConstraint.dateTo.Month + "-" + dateConstraint.dateTo.Day + "T00:00:00.000-05:00'</date_to>\n\t\t\t\t" : "") +
                             "</constrain_by_date>\n\t\t"
                     }
                     queryxml += "</item>\n";
                 }
             }
 
             queryxml +="\t</panel>\n"
 
         }
 
         queryxml += "\t</query_definition>";
 
         return queryxml
     },
 };
 
 
 i2b2.MedCo.QT.ctrlr.appendPanel = function(){
     // Each element (row) visualized on a panel is bound either to a concept (which can
     // be either sensitive or non-sensitive) or to a list of variant ids (always sensitive).
 
     // create a new panel, add it to the list of panels and bind to it model, view and controller
     var panel = {};
     panel.view = {};
     panel.ctrlr = {};
     panel.model = {};
     i2b2.MedCo.QT.panels.push(panel);
 
 
     // ------ initialize the model of the panel ------
     panel.model = {
         // indicates whether the panel is excluded or not
         "exclude": false,
 
         // contains a list of {"sensitive": bool, "values"=[ list of concepts/variant ids bound to i-th row of the panel ]}
         "content": [],
 
         // date constraint model and controller (to show the popup)
         "date": {},
 
         // id of the whole html panel
         "panelId": 'MedCo-QueryPanel' + currId,
 
         // id of the html panel containing dropped concepts
         "conceptPanelId": "MedCo-QueryPanelConcepts" + currId
     };
     currId++;
     // bind the panel to a date constraint model
     i2b2.MedCo.QT.dateConstraint.ctrlr.init(panel)
 
 
     // ------ initialize the view of the panel ------
     document.getElementById("MedCo-QueryPanels").appendChild(htmlToElement(
         "<div class='MedCo-QueryPanel' id='" + panel.model.panelId + "'>" +
             "<div class='MedCo-QueryPanelHeader'>" +
                 "<div class='delete'>" +
                     "<a onclick='i2b2.MedCo.QT.ctrlr.deletePanel(this)' class='queryPanelButton queryPanelButtonHover'>" +
                         "<img src='js-i2b2/cells/CRC/assets/QryTool_b_clear.gif' alt='Clear' />" +
                     "</a>" +
                 "</div>"+
                 "<div class='groupId'>Group " + i2b2.MedCo.QT.panels.length + "</div>" +
             "</div>" +
 
             "<div class='MedCo-QueryPanelOptions'>" +
                 "<div class='date'>" +
                     "<a onclick='i2b2.MedCo.QT.ctrlr.showDateConstraint(this)' title='Select the date range for this group's criterion to have occured within...'>Dates</a>"+
                 "</div>" +
                 "<div class='occur'>" +
                     // <!--<a id="A_11" href="JavaScript:i2b2.CRC.ctrlr.QT.panelControllers[0].showOccurs()" title="Select the minimum number of times this group's criterion has occured...">Occurs &gt; <span id="SPAN_12">0</span>x</a>-->
                 "</div>" +
                 "<div class='exclude'>" +
                     "<a onclick='i2b2.MedCo.QT.ctrlr.excludePanel(this)' title='Exclude records matching this group\'s criteria...'>Exclude</a>" +
                 "</div>" +
             "</div>" +
 
             <!-- Concepts are dropped here -->
             "<div class='MedCo-QueryPanelConcepts' id='" + panel.model.conceptPanelId + "'>" +
             "</div>"  +
         "</div>"));
 
     // // create and add the div for the dropped concepts
     i2b2.sdx.Master.AttachType(panel.model.conceptPanelId , 'CONCPT', {dropTarget: true});
     i2b2.sdx.Master.setHandlerCustom(panel.model.conceptPanelId, 'CONCPT', 'DropHandler', function (sdxData) {panel.ctrlr.doDrop(sdxData);});
 
     /* Instantiate a ContextMenu for this panel*/
     YAHOO.util.Event.onContentReady(panel.model.conceptPanelId, function () {
         var conceptContextMenu = new YAHOO.widget.ContextMenu(
             panel.model.conceptPanelId+"ContextMenu",
             {
                 trigger: document.getElementById(panel.model.conceptPanelId).childNodes,
                 itemdata: ["Delete"],
                 lazyload: true
             }
         );
         // whenever the content of the panel changes, update the trigger property
         $(panel.model.conceptPanelId).on("DOMSubtreeModified",function(){
             conceptContextMenu.cfg.setProperty("trigger", document.getElementById(panel.model.conceptPanelId).childNodes);
         });
 
         function onContextMenuClick(p_sType, p_aArgs) {
             //p_aArgs[1]: MenuItem instance that was the target of the "click" event.
 
             var oItem = p_aArgs[1], // The MenuItem that was clicked
                 oTarget = this.contextEventTarget,
                 oLI;
 
             if (oItem) {
                 // todo: also verify the class (sdxDefaultCONCPT)?
                 oLI = oTarget.nodeName.toUpperCase() == "DIV" ?
                     oTarget : YAHOO.util.Dom.getAncestorByClassName(oTarget, "sdxDefaultCONCPT");
 
 
                 switch (oItem.index) {
                     case 0:     // Delete
                         // remove the concept from the view and from the model
                         var panel_view = document.getElementById(panel.model.conceptPanelId)
                         var index = Array.from(panel_view.children).indexOf(oLI)
                         panel.model.content.splice(index, 1)
                         panel_view.removeChild(oLI)
                         break;
                     // add here other cases if there are more menu items
                 }
 
             }
         }
 
         // "render" event handler for the ewe context menu
         function onContextMenuRender(p_sType, p_aArgs) {
             //  Add a "click" event handler to the ewe context menu
             this.subscribe("click", onContextMenuClick);
         }
         conceptContextMenu.subscribe("render", onContextMenuRender);
         // a bit rude bug fix... (hide menu when clicking on the panel)
         document.getElementById(panel.model.conceptPanelId).onclick = function () {conceptContextMenu.hide.call(conceptContextMenu)}
     });
 
     panel.view.appendConcept = function (concept, output){
         var conceptDiv =
             "<div class='sdxDefaultCONCPT'>" +
                 ((panel.model.exclude) ? "<span title='This item is being excluded' class='itemExclude'>NOT</span>" : "") +
                 "<img src='js-i2b2/cells/ONT/assets/sdx_ONT_CONCPT_leaf.gif'>" +
                 concept +
                 ((output)? (" (<output>...</output>)") : "") +
             "</div>";
         // var panel.model.conceptPanelId = panel.view.getElementsByClassName('MedCo-QueryPanelConcepts')[0].id;
         var conceptPanel = document.getElementById(panel.model.conceptPanelId)
         conceptPanel.innerHTML += conceptDiv;
         return conceptPanel.lastChild
     };
 
     panel.view.clear = function(){
         panel.model.exclude = false;
         var excludeButton = document.getElementById(panel.model.panelId).getElementsByClassName("exclude")[0]
         excludeButton.style.textDecoration = panel.model.exclude? "underline":"none";
 
         var concepts = document.getElementById(panel.model.conceptPanelId);
         while (concepts.firstChild) {
             concepts.removeChild(concepts.firstChild);
         }
     };
 
     // ------ initialize the controller ------
     panel.ctrlr.doDrop = function (sdxData) {
         var concept = sdxData[0];	// only interested in first record
 
         // CHECK: some useful functions:
         // alert(i2b2.h.getXNodeVal(sdxData.origData.xmlOrig, "level"))
         // alert(Object.getOwnPropertyNames(sdxData.origData));
 
         // optimization to prevent requerying the hive for new results if the input dataset has not changed
         // i2b2.ExampTabs.model.dirtyResultsData = true;
 
         // check whether to show a popup or directly append the concept
         switch(concept.sdxInfo.sdxDisplayName) {
             case "Gene Name":
                 i2b2.MedCo.popups.ByGene.ctrlr.show(i2b2.MedCo.QT.panels.indexOf(panel));
                 return;
             case "Protein Position":
                 i2b2.MedCo.popups.ByProteinPosition.ctrlr.show(i2b2.MedCo.QT.panels.indexOf(panel));
                 return;
             case "Variant Name":
                 i2b2.MedCo.popups.ByVariantName.ctrlr.show(i2b2.MedCo.QT.panels.indexOf(panel));
                 return;
         }
 
         var keyval = concept.sdxInfo.sdxKeyValue;
         var sensitive = !keyval.includes("nonsensitive") && !keyval.includes("non-sensitive");
         var conceptModel = sensitive ? concept.origData.basecode.split(":")[1] : (concept.origData.key).replace(/</g,"&lt;");
-        panel.ctrlr.appendConcept(concept.sdxInfo.sdxDisplayName, [conceptModel], sensitive, false);
+        panel.ctrlr.appendConcept(concept.sdxInfo.sdxDisplayName, [conceptModel], sensitive, false, false);
     };
 
-    panel.ctrlr.appendConcept = function(conceptView, conceptModel, sensitive, output){
+    panel.ctrlr.appendConcept = function(conceptView, conceptModel, sensitive, already_encrypted, output){
         // conceptView: what to show in the panel
         // conceptModel: what to save in the model
         // sensitive: boolean to denote if the concept is sensitive
+        // already_encrypted: boolean to denote if the value has to be encrypted or not (note: variant ids are fetched already encrypted)
 
         var concept = {};
         concept.view = {};
         concept.model = {};
 
         // show the dropped concept to the user
         concept.view = panel.view.appendConcept(conceptView, output);
 
         // save the dropped concept to the model of the panel
         concept.model = {
             "sensitive": sensitive,
+            "already_encrypted": already_encrypted,
             "values": conceptModel
         };
         panel.model.content.push(concept.model);
 
         if (sensitive) {
             // add it in the list of things to be encrypted
             i2b2.MedCo.ctrlr.background.toBeEncrypted(conceptModel)
         }
 
         return concept
     };
 
     panel.ctrlr.clear = function(){
         panel.model.exclude = false;
         panel.model.content = [];
         panel.view.clear()
     };
 
     panel.ctrlr.exclude = function(button){
         // mark the panel as excluded
         panel.model.exclude = !panel.model.exclude;
 
         // underline the text in the button if excluded
         button.style.textDecoration = panel.model.exclude? "underline":"none"
 
         // update the concepts visualization
         var conceptsView = document.getElementById(panel.model.conceptPanelId);
         var conceptsDiv = conceptsView.getElementsByClassName("sdxDefaultCONCPT")
         if (panel.model.exclude) {
             // insert "NOT" in front of the concepts in the div
 
             for (var i = 0; i < conceptsDiv.length; i++) {
                 // <span title="This item is being excluded" class="itemExclude">&nbsp;NOT&nbsp;</span>
                 var not = document.createElement("span")
                 not.className = "itemExclude"
                 not.title = "This item is being excluded"
                 not.innerHTML = "NOT"
 
                 conceptsDiv[i].insertBefore(not, conceptsDiv[i].firstChild);
             }
         }
         else {
             // remove the "NOT" in front of the concepts in the div
             for (var i = 0; i < conceptsDiv.length; i++) {
                 conceptsDiv[i].removeChild(conceptsDiv[i].getElementsByClassName("itemExclude")[0])
             }
         }
     };
 
     panel.ctrlr.delete = function(){
         var index = i2b2.MedCo.QT.panels.indexOf(panel)
 
         if (index == -1){
             alert("Impossible to delete the panel, panel inexistent.")
             return
         }
 
         // delete the panel from the model
         i2b2.MedCo.QT.panels.splice(index, 1)
 
         // delete the panel from the view
         var panels_container = document.getElementById("MedCo-QueryPanels")
         var panels = panels_container.childElements()
         panels_container.removeChild(panels[index]);
 
         // update the group number in the header of the panels
         panels = panels_container.childElements()
         for (var i = 0; i < panels.length; i++) {
             // i2b2.MedCo.QT.panels[i].group = (i + 1);
             var header = panels[i].getElementsByClassName("groupId")[0]
             header.innerHTML = 'Group ' + (i+1);
         }
 
         if (i2b2.MedCo.QT.panels.length != panels.length){
             alert("Something went wrong: model and view are inconsistent.")
         }
     }
 
     panel.ctrlr.isEmpty = function(){
         // check there is at least a row which contains something
         for (var i=0; i < panel.model.content.length; i++) {
             if (panel.model.content[i].values.length > 0) {
                 return false;
             }
         }
         return true;
     }
 };
 
 i2b2.MedCo.QT.ctrlr.deletePanel = function(HTMLelem){
     // HTMLelem: (clicked) html element
 
     // first get the index of the panel
     var index = getPanelIndex(HTMLelem);
     if (index < 0){
         alert("Panel not found");
         return
     }
     // then call the delete function on it
     i2b2.MedCo.QT.panels[index].ctrlr.delete()
 };
 
 i2b2.MedCo.QT.ctrlr.excludePanel = function(HTMLelem){
     // HTMLelem: (clicked) html element
 
     // first get the index of the panel
     var index = getPanelIndex(HTMLelem)
     if (index < 0){
         alert("Panel not found")
         return
     }
     // then call the exclude function on it
     i2b2.MedCo.QT.panels[index].ctrlr.exclude(HTMLelem)
 };
 
 i2b2.MedCo.QT.ctrlr.showDateConstraint = function(HTMLelem){
     var index = getPanelIndex(HTMLelem)
     if (index < 0){
         alert("Panel not found")
         return
     }
     // alert("panel index:"+index)
     i2b2.MedCo.QT.panels[index].model.date.ctrlr.show()
 }
\ No newline at end of file
diff --git a/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_popups.js b/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_popups.js
index 2f1bb7f53..bfdc40c1f 100644
--- a/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_popups.js
+++ b/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_popups.js
@@ -1,1027 +1,1028 @@
 i2b2.MedCo.popups = {};
 i2b2.MedCo.popups.ctrlr = {};
 
 // popups for building the query
 i2b2.MedCo.popups.ByVariantName = {};
 i2b2.MedCo.popups.ByVariantName.ctrlr = {};
 
 i2b2.MedCo.popups.ByGene = {};
 i2b2.MedCo.popups.ByGene.ctrlr = {};
 
 i2b2.MedCo.popups.ByProteinPosition = {};
 i2b2.MedCo.popups.ByProteinPosition.ctrlr = {};
 
 // popup for managing the query type
 i2b2.MedCo.popups.SelectQueryType = {};
 i2b2.MedCo.popups.SelectQueryType.ctrlr = {};
 
 // popup for authentication
 i2b2.MedCo.popups.Authentication = {};
 i2b2.MedCo.popups.Authentication.ctrlr = {};
 
 i2b2.MedCo.popups.ctrlr.init = function (){
     i2b2.MedCo.popups.ByVariantName.ctrlr.init();
     i2b2.MedCo.popups.ByGene.ctrlr.init();
     i2b2.MedCo.popups.ByProteinPosition.ctrlr.init();
 
     i2b2.MedCo.popups.SelectQueryType.ctrlr.init();
 
     i2b2.MedCo.popups.Authentication.ctrlr.init();
 };
 
 i2b2.MedCo.popups.ctrlr.clear = function(){
     i2b2.MedCo.popups.ByVariantName.ctrlr.clear();
     i2b2.MedCo.popups.ByGene.ctrlr.clear();
     i2b2.MedCo.popups.ByProteinPosition.ctrlr.clear();
 
     i2b2.MedCo.popups.SelectQueryType.ctrlr.clear();
 
     i2b2.MedCo.popups.Authentication.ctrlr.clear();
 };
 
 i2b2.MedCo.popups.ctrlr.unload = function() {
     // delete view of everything
     i2b2.MedCo.popups.ByVariantName.ctrlr.unload();
     i2b2.MedCo.popups.ByGene.ctrlr.unload();
     i2b2.MedCo.popups.ByProteinPosition.ctrlr.unload();
 
     i2b2.MedCo.popups.SelectQueryType.ctrlr.unload();
 
     i2b2.MedCo.popups.Authentication.ctrlr.unload();
 };
 
 // Manage the php requests.
 // success:     function that takes as input the response form the server
 // error:       function that takes as input the error code returned by the server
 // phpQuery:    string that contains the path and the parameters of the request
 function phpGETRequest(success, error, phpQuery) {
     // create the request object to send the request and manage the response
     var req = false;
     try {
         // most browsers
         req = new XMLHttpRequest();
     } catch (e) {
         // IE
         try {
             req = new ActiveXObject("Msxml2.XMLHTTP");
         } catch (e) {
             // try an older version
             try {
                 req = new ActiveXObject("Microsoft.XMLHTTP");
             } catch (e) {
                 return false;
             }
         }
     }
     // if the http request obj has not been created then return
     if (!req) return false;
 
 
     // update the request object to act when receiving the response
     req.onreadystatechange = function () {
         if (req.readyState == 4) {
             return req.status === 200 ?
                 success(req.responseText) : error(req.status);
         }
     };
 
     req.open("GET", phpQuery, true);
     req.send(null);
     return req;
 };
 
 
 // Function used to initialize gene, protein and variant popup (they have the same structure).
 // -popup: contains variables used to create the pupup (e.g. title, description)
 // -fetchParametersQuery: php query used retrieve the parameters (e.g. genes, proteins or variants). Contains
 //                      "&paramValue" that must be filled with the value of the parameter selected from the popup
 // -fetchVariantsQuery: the final objective of the popup is to fetch the variants. This should be the path to the php
 //                  file that fetches the variants from the database.
 i2b2.MedCo.popups.ctrlr.MedCo_queryPopupInit = function (fetchParametersQuery, fetchVariantsQuery, popup, ctrlr){
     // ------ Initialize the model ------
     var model = {};
     model.choiceList = []; // here is stored the list of suggested parameters
     // the panel number is passed to the popup when opened (so to bind the popup with a panel)
     model.panelIndex = 0;
 
     // ------  Initialize the view  ------
     popup.Id = "MedCo_" + popup.name + "Popup"
 
     popup.paramInputBoxId = "search" + popup.name + "InputBox";
     popup.heteroId = "heterozygous" + popup.name + "Popup";
     popup.homoId = "homozygous" + popup.name + "Popup";
     popup.unknId = "unknown" + popup.name + "Popup";
 
     document.getElementById("MedCo-CONTENT").appendChild(htmlToElement(
         "\n<div id='" + popup.Id + "' style='visibility: collapse;'>" +
             "<div class='hd'>" + popup.text.title + "</div>" +
             "<div class='bd'>" +
                 "<p>" + popup.text.description + "</p>"+
                 "<div class='MedCo_popupParametersSelection'>"+
                     "<div class='parameterRow'>"+
                         "<div>" + popup.text.paramName + "</div>"+
                         "<div>"+
                            "<input type='search' id='" + popup.paramInputBoxId + "' >" +
                         "</div>"+
                     "</div>"+
                     "<br>"+
                     "<div class='parameterRow'>"+
                         "<div> Zygosity* </div>"+
                         "<div class='zygosityListPopup'>"+
                             "<label><input type='checkbox' id='" + popup.heteroId + "'>Heterozygous</label>"+
                             "<label><input type='checkbox' id='" + popup.homoId + "'>Homozygous</label>"+
                             "<label><input type='checkbox' id='" + popup.unknId + "'>Unknown</label>"+
                         "</div>"+
                     "</div>"+
                 "</div>"+
             "</div>"+
         "</div>"));
 
     var view = {};
     view.popup = document.getElementById(popup.Id);
     view.inputBox = document.querySelector("#"+ popup.Id + " #" +popup.paramInputBoxId);
     view.zygosityList = {
         heterozygousCheckbox: document.querySelector("#"+ popup.Id + " #" + popup.heteroId),
         homozygousCheckbox: document.querySelector("#"+ popup.Id + " #" + popup.homoId),
         unknownCheckbox: document.querySelector("#"+ popup.Id + " #" + popup.unknId)
     };
 
     // autocompletion for the inputBox
     new autoComplete({
         cache: false,
         selector: '#' + popup.paramInputBoxId,
         minChars: 1,
         source: function(term, suggest){
             term = term.toLowerCase();
             var matches = [];
             for (var i=0; i<model.choiceList.length; i++){
                 if (~model.choiceList[i].toLowerCase().indexOf(term)) {
                     matches.push(model.choiceList[i]);
 
                     // show only up to 20
                     if (matches.length>20) break
                 }
             }
             suggest(matches);
         }
     });
 
 
     // ------  Initialize the controller  ------
 
     // function used to check if the input box content reflect the selected option in the dropdown list
     view.inputBox.Validate = function (){
         var parameter = view.inputBox.value.replace(/\s/g, '')
         if (parameter!="" && model.choiceList.includes(view.inputBox.value)){
             return true
         }
         // The user has still to pick one from the dropdown list
         alert("Please, write and pick a " + popup.name + " from the dropdown list.");
         return false;
     };
 
     view.zygosityList.Validate = function (){
         if (view.zygosityList.heterozygousCheckbox.checked == false &&
             view.zygosityList.homozygousCheckbox.checked == false &&
             view.zygosityList.unknownCheckbox.checked == false) {
             alert("Please, select at least one zygosity option.");
             return false;
         }
         return true;
     };
 
 
     // fetchParameters manage the fetch of the suggested parameters of the query (e.g. genes, proteins, variants)
     ctrlr.fetchParameters = {
         // if previousParameter (which stores the "old" view.inputBox content) stays the same for a certain period
         // of time then the user stopped writing => I retrieve from the database the matching parameters
         previousParameter: "",
         // here I store the executed queries so to avoid repeating it
         queriedParameters: [""],
         // here I store the timeout (so that I can stop it when I want) used to check when the user stops writing
         timeout: null,
         // waitThenRun allows you to wait for the user to finish writing before running the query
         waitThenRun: function () {
             // we call waitThenRun until the user stops writing
 
             // stop the previous call (every new digits trigger a fetchParameters.run() call)
             clearTimeout(ctrlr.fetchParameters.timeout);
 
             // take the current value removing whitespaces
             var currParameter = view.inputBox.value.replace(/\s/g, '');
 
             if (ctrlr.fetchParameters.queriedParameters.includes(currParameter)) {
                 // if it is equal to a previous query then I already have all the matching ones => just update
                 // the dropdown list (simulate onchange to trigger the autocompletion)
                 ctrlr.fetchParameters.previousParameter = currParameter;
                 view.inputBox.dispatchEvent(new Event('onchange'));
                 return;
             }
 
             if (currParameter != ctrlr.fetchParameters.previousParameter) {
                 // if the current parameter is different from the previous one then wait for the user to finish
                 // to write
                 ctrlr.fetchParameters.previousParameter = currParameter;
                 ctrlr.fetchParameters.timeout = setTimeout(ctrlr.fetchParameters.waitThenRun, 500);
                 return;
             }
 
             // If you ended up here then the user stopped writing and we can execute the query
 
             // store the current query so to avoid repeating it
             ctrlr.fetchParameters.queriedParameters.push(currParameter); // todo not fault tolerant (you store it before receiving the response of the query...)
             ctrlr.fetchParameters.run();
         },
 
         run: function () {
             var currParameter = view.inputBox.value.replace(/\s/g, '');
             var success = function (responseText) {
                 if (responseText.indexOf("error")>=0){
                     alert(responseText)
                     return;
                 }
 
                 // merge the choice list with the new options
                 var merged = new Set(model.choiceList.concat(JSON.parse(responseText)));
                 model.choiceList = [...merged]; // convert to list (after evaluating the set)
                 model.choiceList.sort()
 
                 // update showed list (by pretending there a keyup event)
                 view.inputBox.dispatchEvent(new Event('onchange'));
             };
             var error = function (err) {
                 alert("Error when trying to retrieve the " + popup.name + " values from the database: " + err)
             };
 
             var phpQuery = fetchParametersQuery.replace("$paramValue", currParameter);
             phpGETRequest(success, error, phpQuery);
         }
     };
 
     // fetchVariants manage the fetch of the variants ids (which is the final goal of the popup)
     ctrlr.fetchVariants = {
         run: function () {
             var parameterValue = view.inputBox.value;
             var zygosyty = [];
             if (view.zygosityList.heterozygousCheckbox.checked == true) {
                 zygosyty.push("Heterozygous")
             }
             if (view.zygosityList.homozygousCheckbox.checked == true) {
                 zygosyty.push("Homozygous")
             }
             if (view.zygosityList.unknownCheckbox.checked == true) {
                 zygosyty.push("Unknown")
             }
 
 
             var panel = i2b2.MedCo.QT.panels[model.panelIndex];
             // show the variants to the user
             var conceptView = popup.text.panelParam + parameterValue;
             var conceptModel = []; // still nothing to be stored (we have to wait of the response)
-            var sensitive = false; // it is sensitive but it does not need to be encrypted since already encrypted in the db
+            var sensitive = true; // it is sensitive but it is already encrypted in the db
+            var already_encrypted = true;
             var output = true;
-            var concept = panel.ctrlr.appendConcept(conceptView, conceptModel, sensitive, output);
+            var concept = panel.ctrlr.appendConcept(conceptView, conceptModel, sensitive, already_encrypted, output);
 
             var success = function (responseText) {
                 if (responseText.indexOf("error")>=0){
                     alert(responseText)
                     return;
                 }
 
                 var response = JSON.parse(responseText);
                 // var panel = i2b2.MedCo.QT.panels[model.panelIndex]
 
                 // update the model and the view of the concept
                 concept.model.values = response.variants;
                 concept.view.getElementsByTagName("output")[0].innerHTML = response.variants.length;
                 // i2b2.MedCo.ctrlr.background.toBeEncrypted(response.variants); // the variant is encrypted and stored in the db so it is already fetched encrypted
 
                 // I received the response so decrease the counter
                 i2b2.MedCo.ctrlr.pendingVariantsQueries  -= 1;
             };
             var error = function (err) {
                 alert("Error when trying to retrieve the variants from the database: " + err)
             };
 
             // increase the number of responses I should wait for
             i2b2.MedCo.ctrlr.pendingVariantsQueries  += 1;
 
             // The panel number will be returned with the response so to bind a query to a specific panel (if the
             // query is very slow it could happen that the user starts two queries in parallel which could be related
             // to two different panels).
             var phpQuery =
                 fetchVariantsQuery.replace("$paramValue", parameterValue) +
                 "&zygosity[]=" +  zygosyty.join("&zygosity[]="); // build the array of zygosity options
             phpGETRequest(success, error, phpQuery);
         }
     };
 
     // Popup 'cancel' and 'ok' handlers
     ctrlr.handleCancel = function() {
         // When the popup is closed just call the "cancel" on the YAHOO popup
         this.cancel();
     };
     ctrlr.handleOk = function() {
         // When the user clicks on "ok", check the query parameters and fetch the variants
 
         // validate the fields
         if (! view.inputBox.Validate()){return;}
         if (! view.zygosityList.Validate()){return;}
 
         // run the query to retrieve all the annotations with the specified parameters and zygosyty
         ctrlr.fetchVariants.run();
         this.hide()
     };
 
     // clear the popup fields
     ctrlr.clear = function(){
         view.inputBox.value = "";
         view.zygosityList.heterozygousCheckbox.checked = false;
         view.zygosityList.homozygousCheckbox.checked = false;
         view.zygosityList.unknownCheckbox.checked = false;
     };
 
     ctrlr.unload = function(){
         // destroy the html elements
         view.popup.parentNode.removeChild(view.popup);
     }
 
     // ------  Register controller functions on view elements  ------
 
     // when the user writes in the inputBox you have to run a query to fetch the parameters
     view.inputBox.addEventListener("keyup", ctrlr.fetchParameters.waitThenRun);
 
     // Create the popup with YAHOO.widget
     view.dialog = new YAHOO.widget.SimpleDialog(popup.Id, {
         draggable: true,
         zindex: 10000,
         width: "500px",
         // height: "200px",
         autofillheight: "body",
         constraintoviewport: true,
         context: ["showbtn", "tl", "bl"],
         fixedcenter: true,
         modal: true,
         buttons: [{
             text: "OK",
             handler: ctrlr.handleOk,
             isDefault: true
         }, {
             text: "Cancel",
             handler: ctrlr.handleCancel
         }]
     });
 
     ctrlr.show = function(panelIndex) {
         // show the YAHOO.widget popup
         // ctrlr.clear() // clear the fields
         model.panelIndex = panelIndex;
         view.dialog.render(document.body);
         view.dialog.show();
     };
 }
 
 
 i2b2.MedCo.popups.ByGene.ctrlr.init = function (){
     // define the php queries and insert $something where the parameters will be inserted
     // note: these formats must conform what the relative php files expects as parameters
     var fetchParametersQuery = "js-i2b2/cells/plugins/MedCo/php/fetchGenes.php?" +
         "gene=$paramValue&" +
         "limit=20",  // is it ok 20?
 
         fetchVariantsQuery = 'js-i2b2/cells/plugins/MedCo/php/fetchVariants.php?' +
             'query_type=gene_and_zygosity&' +
             'gene_value=$paramValue', // note the list "&zygosity[]=" of options will be added afterward
         popup = {};
 
     popup.name = "gene"
 
     // define the text for the popup
     popup.text = {}
     popup.text.title = "Search by gene";
     popup.text.description = "Use the gene name box to specify the set of variants for which to search. When you " +
         "begin typing in the search box below some matching options will appear.";
     popup.text.paramName = "Gene Name*";
     popup.text.panelParam = "Gene: ";
 
     i2b2.MedCo.popups.ctrlr.MedCo_queryPopupInit(fetchParametersQuery, fetchVariantsQuery, popup, i2b2.MedCo.popups.ByGene.ctrlr);
 };
 
 
 i2b2.MedCo.popups.ByProteinPosition.ctrlr.init = function(){
     // define the php queries and insert $something where the parameters will be inserted
     // note: these formats must conform what the relative php files expects as parameters
     var fetchParametersQuery = "js-i2b2/cells/plugins/MedCo/php/fetchProteinPositions.php?" +
         "proteinPosition=$paramValue&" +
         "limit=20",  // is it ok 20?
 
         fetchVariantsQuery = 'js-i2b2/cells/plugins/MedCo/php/fetchVariants.php?' +
             'query_type=annotation_and_zygosity&' +
             'annotation_name=Protein_position&' +
             'annotation_value=$paramValue', // note the list "&zygosity[]=" of options will be added afterward
         popup = {};
 
     popup.name = "proteinPosition";
 
     // define the text for the popup
     popup.text = {}
     popup.text.title = "Search by protein position";
     popup.text.description = "Use the protein position annotation box to specify the variants for which to search. " +
         "When you begin typing in the search box below some matching options will appear.";
     popup.text.paramName = "Protein Position*";
     popup.text.panelParam = "Protein position: ";
     i2b2.MedCo.popups.ctrlr.MedCo_queryPopupInit(fetchParametersQuery, fetchVariantsQuery, popup, i2b2.MedCo.popups.ByProteinPosition.ctrlr);
 };
 
 
 i2b2.MedCo.popups.ByVariantName.ctrlr.init = function(){
     // define the php queries and insert $something where the parameters will be inserted
     // note: these formats must conform what the relative php files expects as parameters
     var fetchParametersQuery = "js-i2b2/cells/plugins/MedCo/php/fetchVariantNames.php?" +
         "variant_name=$paramValue&" +
         "limit=20",  // is it ok 20?
 
         fetchVariantsQuery = 'js-i2b2/cells/plugins/MedCo/php/fetchVariants.php?' +
             'query_type=variantName_and_zygosity&' +
             'variant_name=$paramValue', // note the list "&zygosity[]=" of options will be added afterward
         popup = {};
 
     popup.name = "variantName"
 
     // define the text for the popup
     popup.text = {}
     popup.text.title = "Search by variant name";
     popup.text.description = "Use the variant name box to specify the variant for which to search, according to the " +
         "HGVS format (e.g. 10:100150517:G>A). When you begin typing in the search box below some matching options " +
         "will appear.";
     popup.text.paramName = "Variant Name*";
     popup.text.panelParam = "Variant ID: ";
     i2b2.MedCo.popups.ctrlr.MedCo_queryPopupInit(fetchParametersQuery, fetchVariantsQuery, popup, i2b2.MedCo.popups.ByVariantName.ctrlr);
 };
 
 i2b2.MedCo.popups.SelectQueryType.ctrlr.init  = function(){
     var PopupId = "MedCo-SelectQueryTypePopup";
     var queryNameId = "MedCo-QueryName";
     var queryTypeId = "MedCo-QueryType";
 
     // ------  Initialize the view  ------
     document.getElementById("MedCo-CONTENT").appendChild(htmlToElement(
         "<div id='" + PopupId  + "' class='MedCo-Popup QueryTypePopup'>" +
             "<div class='hd'>Run Query</div>" +
             "<div class='bd'>" +
 
                 "<div class='container'>" +
                     "<div>Please type a name for the query:</div>" +
                     "<input id='" + queryNameId + "'>" +
 
                     "<br><br>" +
 
                     "<div>Please check the query result type(s):</div>" +
                     "<div id='" + queryTypeId + "'>" +
                         "<label><input value='PATIENTSET' type='radio' name='queryType'>Patient set</label>" +
                         "<label><input value='PATIENT_COUNT_XML' checked='checked' type='radio' name='queryType'> Number of patients </label>" +
                     "</div>" +
                 "</div>" +
 
             "</div>" +
         "</div>"
     ));
 
     var view = {};
     view.popup = document.getElementById(PopupId);
     view.queryName = document.querySelector("#"+ PopupId + " #" + queryNameId);
     view.queryTypes = [];
 
     // extract the pointer to all the input checkboxes representing the query types
     var types = document.querySelector("#"+ PopupId + " #" + queryTypeId).children;
     for (var i = 0; i < types.length; i++) {
         view.queryTypes.push(types[i].children[0]) // discard the <label>
     }
 
     // ------  Initialize the controller  ------
     var ctrlr = i2b2.MedCo.popups.SelectQueryType.ctrlr;
 
     // Popup 'cancel' and 'ok' handlers
     ctrlr.handleCancel = function() {
         // When the popup is closed just call the "cancel" on the YAHOO popup
         this.cancel();
     };
     ctrlr.handleOk = function() {
         var queryName = view.queryName.value;
         var queryType;
         // var budget = 100;
 
         // validate query name
         if(queryName == ""){
             alert("Please insert a valid query name.");
             return
         }
         // get and validate query type
         var valid = false;
         for (var i = 0; i < view.queryTypes.length; i++){
             if (view.queryTypes[i].checked){
                 queryType = view.queryTypes[i].value;
                 valid = true;
                 break
             }
         }
         if (!valid) {
             alert("Please select at least one query type.");
             return
         }
 
         // run the query (after waiting to receive and encrypt all the variant ids)
         i2b2.MedCo.QT.query.waitThenRun(queryName, queryType);
 
         this.hide()
     };
 
     // clear the popup fields
     ctrlr.clear = function(){
         view.queryName.value = "";
     };
 
     ctrlr.unload = function(){
         // destroy the html elements
         view.popup.parentNode.removeChild(view.popup);
     };
 
     // ------  Register controller functions on view elements  ------
     // Create the popup with YAHOO.widget
     view.dialog = new YAHOO.widget.SimpleDialog(PopupId, {
         draggable: true,
         zindex: 10000,
         width: "400px",
         // height: "200px",
         autofillheight: "body",
         constraintoviewport: true,
         context: ["showbtn", "tl", "bl"],
         fixedcenter: true,
         modal: true,
         buttons: [{
             text: "OK",
             handler: ctrlr.handleOk,
             isDefault: true
         }, {
             text: "Cancel",
             handler: ctrlr.handleCancel
         }]
     });
 
     ctrlr.show = function() {
         // check at least one panel is not empty
         var panels = i2b2.MedCo.QT.panels;
         var empty = true;
         for (var i=0; i<panels.length; i++){
             if (!panels[i].ctrlr.isEmpty()){
                 empty = false;
             }
         }
         if(empty){
             alert("You must enter at least one concept to run a query");
             return
         }
 
         // set the default name for the query
         view.queryName.value = i2b2.MedCo.QT.query.defaultQryName();
 
         // show the YAHOO.widget popup
 
         view.dialog.render(document.body);
         view.dialog.show();
     };
 };
 
 
 // Mock authentication popup. It will be used to authenticate the user to the PM cell by using the private key
 i2b2.MedCo.popups.Authentication.ctrlr.init  = function(){
     var PopupId = "MedCo-Authentication";
 
     // ------  Initialize the view  ------
     document.getElementById("MedCo-CONTENT").appendChild(htmlToElement(
         "<div id='" + PopupId  + "' class='MedCo-Popup QueryTypePopup'>" +
             "<div class='hd'>Authentication (mock popup)</div>" +
             "<div class='bd'>" +
                 "<div class='container'>" +
                     "<div>Please load your private key</div>" +
                 "</div>" +
             "</div>" +
         "</div>"
     ));
 
     var view = {};
     view.popup = document.getElementById(PopupId);
 
     // ------  Initialize the controller  ------
     var ctrlr = i2b2.MedCo.popups.Authentication.ctrlr;
 
     // Popup 'cancel' and 'ok' handlers
     ctrlr.handleCancel = function() {
         // When the popup is closed just call the "cancel" on the YAHOO popup
         this.cancel();
     };
     ctrlr.handleOk = function() {
         this.hide()
     };
 
     // clear the popup fields
     ctrlr.clear = function(){
     };
 
     ctrlr.unload = function(){
         // destroy the html elements
         view.popup.parentNode.removeChild(view.popup);
     };
 
     // ------  Register controller functions on view elements  ------
     // Create the popup with YAHOO.widget
     view.dialog = new YAHOO.widget.SimpleDialog(PopupId, {
         draggable: true,
         zindex: 10000,
         width: "400px",
         // height: "200px",
         autofillheight: "body",
         constraintoviewport: true,
         context: ["showbtn", "tl", "bl"],
         fixedcenter: true,
         modal: true,
         buttons: [{
             text: "OK",
             handler: ctrlr.handleOk,
             isDefault: true
         }, {
             text: "Cancel",
             handler: ctrlr.handleCancel
         }]
     });
 
     ctrlr.show = function() {
         // show the YAHOO.widget popup
 
         view.dialog.render(document.body);
         view.dialog.show();
     };
 };
 
 
 
 // // ANNOTATION POPUP
 // i2b2.MedCo.ctrlr.popups.ByAnnotation = {
 //     dialog: null,
 //
 //     // variable to access easily the popup's window
 //     window: $("MedCo_annotationPopup"),
 //
 //     // input box in which the user will write. It is an <input type="search"> element
 //     annotationNameInputBox: document.querySelector("#searchAnnotationNameInputBox"),
 //
 //     // selection list to display the matching annotation names. It is a <select> element
 //     annotationNameList: document.querySelector("#annotationNameList"),
 //
 //     // input box in which the user will write. It is an <input type="search"> element
 //     annotationValueInputBox: document.querySelector("#searchAnnotationValueInputBox"),
 //
 //     // selection list to display the matching annotation values. It is a <select> element
 //     annotationValueList: document.querySelector("#annotationValueList"),
 //
 //     // selection list with the 3 predefined options
 //     zygosityList: {
 //         heterozygousCheckbox:null,
 //         homozygousCheckbox:null,
 //         unknownCheckbox:null
 //     },
 //
 //     // variable used for the popup to know to which panel it is bound
 //     panelNumber: 0,
 //
 //     // initialize the annotation popup
 //     init: function(){
 //         var context = i2b2.MedCo.ctrlr.popups.ByAnnotation;
 //
 //         context.window = $("MedCo_annotationPopup");
 //
 //         context.annotationNameInputBox = document.querySelector("#searchAnnotationNameInputBox");
 //         context.annotationNameList = document.querySelector("#annotationNameList");
 //
 //         context.annotationValueInputBox = document.querySelector("#searchAnnotationValueInputBox");
 //         context.annotationValueList = document.querySelector("#annotationValueList");
 //
 //         // the three checkboxes
 //         context.zygosityList.heterozygousCheckbox = document.querySelector("#heterozygousAnnotationNamePopup");
 //         context.zygosityList.homozygousCheckbox = document.querySelector("#homozygousAnnotationNamePopup");
 //         context.zygosityList.unknownCheckbox = document.querySelector("#unknownAnnotationNamePopup");
 //
 //         // update the scrolldown list every time the user digits chars
 //         context.annotationNameInputBox
 //             .addEventListener("keyup",
 //                 context.getAnnotationNames.run
 //             );
 //
 //         context.annotationValueInputBox
 //             .addEventListener("keyup",
 //                 context.getAnnotationValues.run
 //             );
 //
 //         context.panelNumber = 0;
 //
 //         context.getAnnotationNames.path = 'js-i2b2/cells/plugins/MedCo/php/getAnnotationNames.php';
 //         context.getAnnotationValues.path = 'js-i2b2/cells/plugins/MedCo/php/getAnnotationValues.php';
 //         context.getVariants.path = 'js-i2b2/cells/plugins/MedCo/php/getVariants.php';
 //
 //         var handleCancel = function() {
 //             this.cancel();
 //         };
 //
 //         var handleOk = function() {
 //             var context = i2b2.MedCo.ctrlr.popups.ByAnnotation;
 //
 //             // validate the fields
 //             if (! i2b2.MedCo.ctrlr.inputBoxIsOk(context.annotationNameInputBox, context.annotationNameList, "an annotation name")){return;}
 //             if (! i2b2.MedCo.ctrlr.inputBoxIsOk(context.annotationValueInputBox, context.annotationValueList, "an annotation value")){return;}
 //             if (! i2b2.MedCo.ctrlr.zygosityIsOk(context.zygosityList)){return;}
 //
 //             // run the query to retrieve all the annotations with the specified annotation name and zygosyty
 //             i2b2.MedCo.ctrlr.popups.ByAnnotation.getVariants.run();
 //             this.hide()
 //         };
 //
 //         context.dialog = new YAHOO.widget.SimpleDialog("MedCo_annotationPopup", {
 //             draggable: true,
 //             zindex: 10000,
 //             width: "500px",
 //             // height: "200px",
 //             autofillheight: "body",
 //             constraintoviewport: true,
 //             context: ["showbtn", "tl", "bl"],
 //             fixedcenter: true,
 //             modal: true,
 //             buttons: [{
 //                 text: "OK",
 //                 handler: handleOk,
 //                 isDefault: true
 //             }, {
 //                 text: "Cancel",
 //                 handler: handleCancel
 //             }]
 //         });
 //     },
 //
 //     // show the popup
 //     // panelNumber: specifies with which panel is the popup related
 //     show: function(panelNumber) {
 //         var context = i2b2.MedCo.ctrlr.popups.ByAnnotation;
 //
 //         context.panelNumber = panelNumber;
 //         // context.clear();
 //         context.window.show();
 //         context.dialog.render(document.body);
 //         context.dialog.show();
 //     },
 //
 //     // // hide the popup, not needed (events already registered to the various buttons)
 //     // hide: function(){
 //     //     i2b2.MedCo.ctrlr.annotationNamePopup.popups.hide();
 //     //     i2b2.MedCo.ctrlr.annotationNamePopup.dialog.cancel();
 //     // },
 //
 //     // clear (empty) all the elements
 //     clear: function(){
 //         // i2b2.MedCo.ctrlr.annotationNamePopup.annotationNameInputBox.value = "";
 //         // var list = i2b2.MedCo.ctrlr.annotationNamePopup.annotationNameList;
 //         // while (list.hasChildNodes()) {
 //         //     list.removeChild(list.lastChild);
 //         // }
 //         //    todo clear fields?
 //     },
 //
 //     // get the annotation names from the database
 //     getAnnotationNames: {
 //         // Store some variables I need to efficiently manage the request
 //
 //         // path for the php request to retrieve the annotation names
 //         path: 'js-i2b2/cells/plugins/MedCo/php/getAnnotationNames.php',
 //         // if previousAnnotation (which stores the "old" annotationNameInputBox content) stays the same for a certain period
 //         // of time then the user stopped writing => I retrieve from the database the matching annotation names
 //         previousAnnotationName: "",
 //         // here I store the last executed query so to avoid repeating it
 //         lastAnnotationQueried: "",
 //         // here I store the current timeout (so that I can stop it when I want)
 //         timeoutAnnotation: null,
 //         run: function () {
 //             var context = i2b2.MedCo.ctrlr.popups.ByAnnotation.getAnnotationNames;
 //
 //             // (call run until the user stops writing)
 //             // stop the previous call (every new digits trigger a getAnnotationNames() call)
 //             clearTimeout(context.timeoutAnnotation);
 //             // take the current value and check if it is equal to the previous one
 //             var currAnnotationName = i2b2.MedCo.ctrlr.popups.ByAnnotation.annotationNameInputBox.value.replace(/\s/g, ''); // remove whitespaces
 //             if (currAnnotationName == ""){
 //                 // if it is empty then just empty the dropdown list
 //                 var list = i2b2.MedCo.ctrlr.popups.ByAnnotation.annotationNameList;
 //                 while (list.hasChildNodes()) {
 //                     list.removeChild(list.lastChild);
 //                 }
 //                 context.lastAnnotationQueried = "";
 //                 return;
 //             }
 //             if (currAnnotationName == context.lastAnnotationQueried) {
 //                 // if it is equal to the previous query then do nothing
 //                 return;
 //             }
 //             if (currAnnotationName != context.previousAnnotationName) {
 //                 // if they are different then wait for the user to finish to write
 //                 context.previousAnnotationName = currAnnotationName;
 //                 context.timeoutAnnotation = setTimeout(context.run, 500);
 //                 return;
 //             }
 //
 //             // If you ended up here then the user stopped writing and we can execute the query
 //             context.lastAnnotationQueried = currAnnotationName; // store the current query so to avoid repeating it
 //
 //             var success = function (responseText) {
 //                 if (responseText.indexOf("error")>=0){
 //                     alert(responseText)
 //                     return;
 //                 }
 //                 var list = i2b2.MedCo.ctrlr.popups.ByAnnotation.annotationNameList;
 //                 // remove all the previous annotation names from the dropdown list
 //                 while (list.hasChildNodes()) {
 //                     list.removeChild(list.lastChild);
 //                 }
 //                 // todo sort the annotation names
 //                 var receivedAnnotationNames= JSON.parse(responseText);
 //                 for (var i = 0; i < receivedAnnotationNames.length; i++) {
 //                     var opt = document.createElement("option");
 //                     opt.value = receivedAnnotationNames[i];
 //                     opt.innerHTML = receivedAnnotationNames[i];
 //                     list.appendChild(opt);
 //                 }
 //
 //                 // if there was only one match the copy that in the text box
 //                 if (receivedAnnotationNames.length == 1) {
 //                     i2b2.MedCo.ctrlr.popups.ByAnnotation.annotationNameInputBox.value = receivedAnnotationNames[0];
 //                 }
 //             };
 //             var error = function (err) {
 //                 alert("Error when trying to retrieve the annotation names from the database: " + err)
 //             };
 //
 //             var phpQuery =
 //                 context.path +
 //                 "?annotation_name=" + currAnnotationName +
 //                 "&limit=20";  // is it ok 20?
 //             i2b2.MedCo.ctrlr.phpGETRequest(success, error, phpQuery);
 //         }
 //     },
 //
 //     getAnnotationValues: {
 //         // Store some variables I need to efficiently manage the request
 //
 //         // path for the php request to retrieve the annotation valuess
 //         path: 'js-i2b2/cells/plugins/MedCo/php/getAnnotationValues.php',
 //         // if previousAnnotation (which stores the "old" annotationValueInputBox content) stays the same for a certain period
 //         // of time then the user stopped writing => I retrieve from the database the matching annotation valuess
 //         previousAnnotationValue: "",
 //         // here I store the last executed query so to avoid repeating it
 //         lastAnnotationQueried: "",
 //         // here I store the current timeout (so that I can stop it when I want)
 //         timeoutAnnotation: null,
 //         run: function () {
 //             // first check the annotation name has been selected
 //             var context = i2b2.MedCo.ctrlr.popups.ByAnnotation;
 //             if (! i2b2.MedCo.ctrlr.inputBoxIsOk(context.annotationNameInputBox, context.annotationNameList, "an annotation name")){return;}
 //             var annotationName = context.annotationNameInputBox.value;
 //
 //             var context = context.getAnnotationValues;
 //             // (call run until the user stops writing)
 //             // stop the previous call (every new digits trigger a getAnnotationValues() call)
 //             clearTimeout(context.timeoutAnnotation);
 //             // take the current value and check if it is equal to the previous one
 //             var currAnnotationValue= i2b2.MedCo.ctrlr.popups.ByAnnotation.annotationValueInputBox.value.replace(/\s/g, ''); // remove whitespaces
 //             if (currAnnotationValue == ""){
 //                 // if it is empty then just empty the dropdown list
 //                 var list = i2b2.MedCo.ctrlr.popups.ByAnnotation.annotationValueList;
 //                 while (list.hasChildNodes()) {
 //                     list.removeChild(list.lastChild);
 //                 }
 //                 context.lastAnnotationQueried = "";
 //                 return;
 //             }
 //             if (currAnnotationValue == context.lastAnnotationQueried) {
 //                 // if it is equal to the previous query then do nothing
 //                 return;
 //             }
 //             if (currAnnotationValue != context.previousAnnotationValue) {
 //                 // if they are different then wait for the user to finish to write
 //                 context.previousAnnotationValue = currAnnotationValue;
 //                 context.timeoutAnnotation = setTimeout(context.run, 500);
 //                 return;
 //             }
 //
 //             // If you ended up here then the user stopped writing and we can execute the query
 //             context.lastAnnotationQueried = currAnnotationValue; // store the current query so to avoid repeating it
 //
 //             var success = function (responseText) {
 //                 if (responseText.indexOf("error")>=0){
 //                     alert(responseText)
 //                     return;
 //                 }
 //                 var list = i2b2.MedCo.ctrlr.popups.ByAnnotation.annotationValueList;
 //                 // remove all the previous annotation valuess from the dropdown list
 //                 while (list.hasChildNodes()) {
 //                     list.removeChild(list.lastChild);
 //                 }
 //                 // todo sort the annotation values
 //                 var receivedAnnotationValues= JSON.parse(responseText);
 //                 for (var i = 0; i < receivedAnnotationValues.length; i++) {
 //                     var opt = document.createElement("option");
 //                     opt.value = receivedAnnotationValues[i];
 //                     opt.innerHTML = receivedAnnotationValues[i];
 //                     list.appendChild(opt);
 //                 }
 //
 //                 // if there was only one match the copy that in the text box
 //                 if (receivedAnnotationValues.length == 1) {
 //                     i2b2.MedCo.ctrlr.popups.ByAnnotation.annotationValueInputBox.value = receivedAnnotationValues[0];
 //                 }
 //             };
 //             var error = function (err) {
 //                 alert("Error when trying to retrieve the annotation values from the database: " + err)
 //             };
 //
 //
 //             var phpQuery =
 //                 context.path +
 //                 "?annotation_name=" + annotationName +
 //                 "&annotation_value=" + currAnnotationValue +
 //                 "&limit=20";  // is it ok 20?
 //             i2b2.MedCo.ctrlr.phpGETRequest(success, error, phpQuery);
 //         }
 //     },
 //
 //     // run the query to retrieve the id of the annotations
 //     getVariants: {
 //         path: 'js-i2b2/cells/plugins/MedCo/php/getVariants.php',
 //
 //         run: function () {
 //             var context = i2b2.MedCo.ctrlr.popups.ByAnnotation;
 //
 //             var annotationName = context.annotationNameInputBox.value;
 //             var annotationValue = context.annotationValueInputBox.value;
 //             var zygosyty = [];
 //             if (context.zygosityList.heterozygousCheckbox.checked == true) {
 //                 zygosyty.push("Heterozygous")
 //             }
 //             if (context.zygosityList.homozygousCheckbox.checked == true) {
 //                 zygosyty.push("Homozygous")
 //             }
 //             if (context.zygosityList.unknownCheckbox.checked == true) {
 //                 zygosyty.push("Unknown")
 //             }
 //
 //             // show the variants to the user
 //             var concept_div = i2b2.MedCo.ctrlr.createDiv(annotationName + ": " + annotationValue, true);
 //             i2b2.MedCo.view.panels[context.panelNumber].appendChild(concept_div)
 //
 //             var queryType = "annotation_and_zygosity"; // used at the server side to know how to build the query
 //
 //             var success = function (responseText) {
 //                 if (responseText.indexOf("error")>=0){
 //                     alert(responseText)
 //                     return;
 //                 }
 //                 //alert(responseText);
 //                 var response = JSON.parse(responseText);
 //                 for(var i=0; i<response.annotations.length; i++)
 //                 {
 //                     i2b2.MedCo.model.panels[response.panel_number].sensitive.push(response.annotations[i]);
 //                 }
 //                 i2b2.MedCo.ctrlr.background.toBeEncrypted(response.variants);
 //
 //                 // show how many variants have been retrieved
 //                 concept_div.getElementsByTagName("output")[0].innerHTML = response.variants.length;
 //
 //                 // I received the response so decrease the counter
 //                 i2b2.MedCo.ctrlr.pendingAnnotationsQueries  -= 1;
 //             };
 //             var error = function (err) {
 //                 alert("Error when trying to retrieve the variants from the database: " + err)
 //             };
 //
 //             // increase the number of responses I should wait for
 //             i2b2.MedCo.ctrlr.pendingAnnotationsQueries  += 1;
 //
 //             // better pass the panel number too. It will be returned with the response so that I bind it to a
 //             // specific panel. (if the query is very slow it could happen that the user starts two queries in parallel
 //             // which are related to two different panels).
 //             var phpQuery =
 //                 context.getAnnotations.path +
 //                 "?query_type=" + queryType +
 //                 "&panel_number=" + context.panelNumber +
 //                 "&annotation_name=" + annotationName +
 //                 "&annotation_value=" + annotationValue +
 //                 "&zygosity[]=" +  zygosyty.join("&zygosity[]="); // build an array of zygosity options
 //             i2b2.MedCo.ctrlr.phpGETRequest(success, error, phpQuery);
 //         }
 //     }
 // };
\ No newline at end of file
diff --git a/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_tests.js b/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_tests.js
index 75b98a72f..b61cecfba 100644
--- a/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_tests.js
+++ b/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_tests.js
@@ -1,513 +1,513 @@
 i2b2.MedCo.test = {};
 
 i2b2.MedCo.test.ctrlr = {
     // A query is a list of panels. Each panel is a list of parameters. Each parameter is represented as
-    // {"sensitive": boolean, "toBeEncrypted": boolean, "values": {type: "concept/gene/protein", name: "<name>"}}
+    // {"sensitive": boolean, "already_encrypted": boolean, "values": {type: "concept/gene/protein", name: "<name>"}}
     // The "values" field will be substituted by the true values of this parameter (which may need to be fetched from
     // the database). The "name" can be used to retrieve the values of the parameter from the parameter_to_values map
     // (in which we store the values fetched from the database).
 
     // Query used for testing (non sensitive)
     queryTest1: {
         description: [
-            [{"sensitive": false, "toBeEncrypted": false, "values": {type: "concept", name: "Adrenal"}}]
+            [{"sensitive": false, "already_encrypted": false, "values": {type: "concept", name: "Adrenal"}}]
         ],
         definition: null, // here we store the query to be sent (after fetching the needed variants)
     },
 
     // Query used for testing (sensitive)
     queryTest2: {
         description: [
-            [{"sensitive": true, "toBeEncrypted": true, "values": {type: "concept", name: "cutaneous_melanoma"}}]
+            [{"sensitive": true, "already_encrypted": false, "values": {type: "concept", name: "cutaneous_melanoma"}}]
         ],
         definition: null, // here we store the query to be sent (after fetching the needed variants)
     },
 
 
     // Query used for testing (sensitive)
     queryTest3: {
         description: [
-            [{"sensitive": true, "toBeEncrypted": false, "values": {type: "concept", name: "taggedVariantID1"}}]
+            [{"sensitive": true, "already_encrypted": true, "values": {type: "concept", name: "taggedVariantID1"}}]
         ],
         definition: null, // here we store the query to be sent (after fetching the needed variants)
     },
 
     // Query A:
     //  -panel 1:
     //      cutaneous_melanoma
     //  -panel 2:
     //      braf_gene
     //  -panel 3:
     //      protein_600
     queryA: {
         description: [
-            [{"sensitive": true, "toBeEncrypted": true, "values": {type: "concept", name: "cutaneous_melanoma"}}],
-            [{"sensitive": true, "toBeEncrypted": false, "values": {type: "gene", name: "BRAF"}}],
-            [{"sensitive": true, "toBeEncrypted": false, "values": {type: "protein", name: "V600K"}},    // 0
-                {"sensitive": true, "toBeEncrypted": false, "values": {type: "protein", name: "V600E"}}] // 2 (or viceversa)
+            [{"sensitive": true, "already_encrypted": false, "values": {type: "concept", name: "cutaneous_melanoma"}}],
+            [{"sensitive": true, "already_encrypted": true, "values": {type: "gene", name: "BRAF"}}],
+            [{"sensitive": true, "already_encrypted": true, "values": {type: "protein", name: "V600K"}},    // 0
+                {"sensitive": true, "already_encrypted": true, "values": {type: "protein", name: "V600E"}}] // 2 (or viceversa)
         ],
         definition: null, // here we store the query to be sent (after fetching the needed variants)
     },
 
     // Query B:
     // -panel 1:
     //      cutaneous_melanoma
     // -panel 2:
     //      braf_gene
     // -panel 3:
     //      pten_gene, cdkn2a_gene, map2k1_gene, map2k2_gene
     queryB: {
         description: [
-            [{"sensitive": true, "toBeEncrypted": true, "values": {type: "concept", name: "cutaneous_melanoma"}}],
-            [{"sensitive": true, "toBeEncrypted": false,"values": {type: "gene", name: "BRAF"}}], // 91 variants
-            [{"sensitive": true, "toBeEncrypted": false, "values": {type: "gene", name: "PTEN"}},  // 319
-                {"sensitive": true, "toBeEncrypted": false, "values": {type: "gene", name: "CDKN2A"}}, // 117
-                {"sensitive": true, "toBeEncrypted": false, "values": {type: "gene", name: "MAP2K1"}}, // 35
-                {"sensitive": true, "toBeEncrypted": false, "values": {type: "gene", name:"MAP2K2"}}]  // 33
+            [{"sensitive": true, "already_encrypted": false, "values": {type: "concept", name: "cutaneous_melanoma"}}],
+            [{"sensitive": true, "already_encrypted": true,"values": {type: "gene", name: "BRAF"}}], // 91 variants
+            [{"sensitive": true, "already_encrypted": true, "values": {type: "gene", name: "PTEN"}},  // 319
+                {"sensitive": true, "already_encrypted": true, "values": {type: "gene", name: "CDKN2A"}}, // 117
+                {"sensitive": true, "already_encrypted": true, "values": {type: "gene", name: "MAP2K1"}}, // 35
+                {"sensitive": true, "already_encrypted": true, "values": {type: "gene", name:"MAP2K2"}}]  // 33
         ],
         definition: null, // here we store the query to be sent (after fetching the needed variants)
     },
 
     queryB_noPTEN: {
         description: [
-            [{"sensitive": true, "toBeEncrypted": true, "values": {type: "concept", name: "cutaneous_melanoma"}}],
-            [{"sensitive": true, "toBeEncrypted": false,"values": {type: "gene", name: "BRAF"}}], // 91 variants
-            [{"sensitive": true, "toBeEncrypted": false, "values": {type: "gene", name: "CDKN2A"}}, // 117
-                {"sensitive": true, "toBeEncrypted": false, "values": {type: "gene", name: "MAP2K1"}}, // 35
-                {"sensitive": true, "toBeEncrypted": false, "values": {type: "gene", name:"MAP2K2"}}]  // 33
+            [{"sensitive": true, "already_encrypted": false, "values": {type: "concept", name: "cutaneous_melanoma"}}],
+            [{"sensitive": true, "already_encrypted": true,"values": {type: "gene", name: "BRAF"}}], // 91 variants
+            [{"sensitive": true, "already_encrypted": true, "values": {type: "gene", name: "CDKN2A"}}, // 117
+                {"sensitive": true, "already_encrypted": true, "values": {type: "gene", name: "MAP2K1"}}, // 35
+                {"sensitive": true, "already_encrypted": true, "values": {type: "gene", name:"MAP2K2"}}]  // 33
         ],
         definition: null, // here we store the query to be sent (after fetching the needed variants)
     },
 
     // map to store the values of each query parameter (also the fetched variants from the database)
     parameter_to_values: {
         // no need to fetch these
         "Adrenal": ["\\\\CLINICAL_NON_SENSITIVE\\medco\\clinical\\nonsensitive\\Tumor Tissue Site\\Adrenal\\"],
         "cutaneous_melanoma": ["149"],
         "taggedVariantID1": null,
 
         // hardcoded variant ids
         // (25 variants): gene
         // "BRAF": ["-7054948997223410688", "-7054948998062267136", "-7054968999892742144", "-7054948999337337856", "-7054948997064022784", "-7054953138544961536", "-7054948997064020736", "-7054923607457132544", "-7054904773018905600", "-7054898625779855360", "-7054948987408734208", "-7054923379857424384", "-7054917142457610240", "-7054861692282335232", "-7054948050082458624", "-7054922546600210432", "-7054949048695910400", "-7054923381098933248", "-7054861517262417920", "-7054918645662608384", "-7054905185268658176", "-7054904954414166016", "-7054898626853597184", "-7054904932905773056", "-7054861823278837760"],
         // // (58 variants): protein position
         // "-/600": ["-8933802084025738584", "-6486664075878068224", "-5631356589790194688", "-3744382902155078656", "-4243330163464466432", "-8390864270639754240", "-2861998644146466816", "-8933794510723345408", "-2275778788769918976", "-3744380364936704000", "-4847903122799977472", "-3744370070973837312", "-6486663046126103552", "-2862005101596240896", "-8933793458456358912", "-3731886507003209728", "-4243326752186690560", "-3684888714590289920", "-6600247701843995648", "-5707938912580661248", "-6600348525161082880", "-4243327620843826176", "-5707936738253467648", "-3744381594337537024", "-8390871813676067840", "-6486638321073122304", "-8718336899686591488", "-8161767032237320192", "-8718388095730315264", "-6600348471507544064", "-4847902555864297472", "-8718385496201359360", "-3744381715771026432", "-8390900435338128384", "-4243331029974117376", "-8718385510160003072", "-5707941003155992576", "-5707940965541473280", "-3744377054557105152", "-8390878215358377984", "-8161775324644764672", "-8161760075430494208", "-8933792699320889344", "-8933788672755493888", "-8718360110998468096", "-5707941120160295936", "-6600276494231006208", "-8933788638429310976", "-6486653465127809024", "-3744380416476311552", "-3729075172548795136", "-6600294904608320512", "-8933788867136319488", "-5707939282988035072", "-3744381760767524864", "-2275781595497491456", "-8933793225454383104", "-4243329794097277952"],
         // // (14 variants): gene
         // "PTEN": ["-6244734599302213632", "-6244835122005142528", "-6244734615609652992", "-6244731379150482432", "-6244761261385445376", "-6244761331212216320", "-6244803225329855488", "-6244761257090477056", "-6244761165822422016", "-6244761148709661696", "-6244761290443582464", "-6244734719527742464", "-6244803244478955520", "-6244731450050998272"],
         // // (22 variants): gene
         // "CDKN2A": ["-6605707269956960256", "-6605707340823916544", "-6605707363372498944", "-6605707399913269248", "-6605707450345581568", "-6605707366560164864", "-6605707493295259648", "-6605707451419324416", "-6605707339750174720", "-6605707347467692032", "-6605707487054123520", "-6605707304132149248", "-6605703514008055808", "-6605707366560165888", "-6605707438500867072", "-6605707503026037760", "-6605703519225765120", "-6605707607111888896", "-6605707340672917504", "-6605703519376764928", "-6605707351594886144", "-6605707619996790784"],
         // // (9 variants): gene
         // "MAP2K1": ["-4828214681296432128", "-4828266596713621504", "-4828266483970731008", "-4828258079793473536", "-4828266501150601216", "-4828266502224342016", "-4828257969198066688", "-4828266574613577728", "-4828218249340513280"],
         // // (7 variants): gene
         // "MAP2K2": ["-3742593253707344896", "-3742593391179853824", "-3742595392634613760", "-3742581279372079104", "-3742593229011282944", "-3742591331743035392", "-3742581136564416512"],
     },
 
     // time the action started
     startTime: null,
 
     // whether the query has been encrypted
     encrypted: false,
 
     // whether it is already doing something (encrypting or sending the queries)
     doing: "",
 
     // pointer to the interval object so to stop it
     timeinterval: null,
 
     // response of the query
     response: null,
 
     fetchVariantIds: function(){
         // fetch the variant ids needed for the query and store them in the map parameter_to_values
         if (this.doing != ""){
             alert("Already " + this.doing);
             return
         }
         this.doing = "fetching the variant ids...";
 
         var startTime = new Date().getTime();
 
         var query = this.getSelectedQuery().description;
 
         var fetchByGenePHPreq = "js-i2b2/cells/plugins/MedCo/php/fetchVariants.php?" +
             "query_type=gene_and_zygosity&" +
             "gene_value=$geneValue" +
             "&zygosity[]=Heterozygous&zygosity[]=Homozygous&zygosity[]=Unknown";
         var fetchByProteinPHPreq = "js-i2b2/cells/plugins/MedCo/php/fetchVariants.php?" +
             "query_type=protein_position_and_zygosity&" +
             "protein_change_value=$proteinChangeValue" +
             "&zygosity[]=Heterozygous&zygosity[]=Homozygous&zygosity[]=Unknown";
 
         var numFetchedVariants = 0;
         var numResponses = 0;
 
         var success = function (paramName) {
             return function(responseText) {
                 if (responseText.indexOf("error") >= 0) {
                     alert(responseText);
                     return;
                 }
 
                 var response = JSON.parse(responseText);
 
                 // store the fetched variant ids in the map
                 i2b2.MedCo.test.ctrlr.parameter_to_values[paramName] = response.variants;
                 numFetchedVariants += response.variants.length;
                 numResponses++;
             }
         };
         var error = function (err) {
             alert("Error when trying to retrieve the variants from the database: " + err)
         };
 
         var numQueries = 0;
         for (var panel=0; panel< query.length; panel++) {
             for (var parameter = 0; parameter < query[panel].length; parameter++) {
                 var param = query[panel][parameter].values;
                 if (param.type=="gene"){
                     var phpQuery = fetchByGenePHPreq.replace("$geneValue", param.name);
                 }
                 else if (param.type=="protein"){
                     var phpQuery = fetchByProteinPHPreq.replace("$proteinChangeValue", param.name);
                 }
                 else{
                     // no need to fetch variant ids fro this parameter
                     continue;
                 }
 
                 numQueries++;
                 phpGETRequest(success(param.name), error, phpQuery);
             }
         }
 
         document.getElementById("MedCoTest-NumVariantIds").innerHTML = "-";
         document.getElementById("MedCoTest-NumPHPQueriesCurr").innerHTML = 0;
         document.getElementById("MedCoTest-NumPHPQueriesTot").innerHTML = numQueries;
 
         // start timer
         var dothis = function(){
             document.getElementById("MedCoTest-NumVariantIds").innerHTML = numFetchedVariants;
             document.getElementById("MedCoTest-NumPHPQueriesCurr").innerHTML = numResponses;
         };
 
         var done = function(){
             if (numResponses>=numQueries){
                 document.getElementById("MedCoTest-NumVariantIds").innerHTML = numFetchedVariants;
                 return true
             }
             return false
         };
 
         this.startTimer(startTime, "MedCoTest-VariantIdsTime", done, dothis);
     },
 
     encrypt: function(){
         // encrypt the sensitive parameters of the query
         if (this.doing != ""){
             alert("Already " + this.doing);
             return
         }
         var query = this.getSelectedQuery();
         if (query.definition==null) {
             if (!this.defineQuery(query)) {
                 alert("You have to fetch the variants.");
                 return
             }
         }
         query = query.definition;
 
         this.doing = "encrypting...";
 
         var startTime = new Date().getTime();
 
         // clear encryption cache and start encryption
         i2b2.MedCo.ctrlr.background.encryptionCache = {};
         var tot = 0;
         for (var panel = 0; panel < query.length; panel++){
             for (var parameter = 0; parameter < query[panel].length; parameter++){
                 var entry = query[panel][parameter];
                 if (entry.sensitive) {
-                    if (entry.toBeEncrypted) {
+                    if (!entry.already_encrypted) {
                         i2b2.MedCo.ctrlr.background.toBeEncrypted(entry.values);
                         tot += entry.values.length;
                     }
-                    else{
-                        // HACK (avoid encrypting already tagged variants)
-                        for (var i=0; i<entry.values.length; i++) {
-                            i2b2.MedCo.ctrlr.background.encryptionCache[entry.values[i]] = entry.values[i];
-                        }
-                    }
+                    // else{
+                    //     // HACK (avoid encrypting already tagged variants)
+                    //     for (var i=0; i<entry.values.length; i++) {
+                    //         i2b2.MedCo.ctrlr.background.encryptionCache[entry.values[i]] = entry.values[i];
+                    //     }
+                    // }
                 }
             }
         }
         document.getElementById("MedCoTest-EncryptTot").innerHTML = tot;
         document.getElementById("MedCoTest-EncryptCurr").innerHTML = 0;
 
         // start timer
         var dothis = function(){
             document.getElementById("MedCoTest-EncryptCurr").innerHTML = tot - i2b2.MedCo.ctrlr.background.remainingToEncrypt;
         };
 
         var done = function(){
             if (i2b2.MedCo.ctrlr.background.encryptionDone()){
                 i2b2.MedCo.test.ctrlr.encrypted = true;
                 return true
             }
             return false
         };
 
         this.startTimer(startTime, "MedCoTest-EncryptTime", done, dothis);
     },
 
     send: function(){
         if (this.doing != ""){
             alert("Already " + this.doing);
             return
         }
         // check the query has been encrypted
         if (!this.encrypted){
             alert("You have to encrypt the query.")
             return
         }
         this.doing = "sending the query...";
         var startTime = new Date().getTime();
 
         // get query
         var query = this.getSelectedQuery().definition;
 
         // clear panels and put in their model the parameters
         i2b2.MedCo.QT.ctrlr.clear();
         for (var i = 0; i < query.length; i++){
             var panel=query[i];
             for (var j = 0; j < panel.length; j++){
                 i2b2.MedCo.QT.panels[i].model.content.push(panel[j])
             }
         }
 
         var numQueries = this.getNumQueries();
         var numResponses = 0;
         var queryTimes = [];
 
         function sendQuery() {
             var startTime = new Date().getTime();
             this.MedCoparams = {};
             var qryName = i2b2.MedCo.QT.query.defaultQryName() + "|" + "PATIENT_COUNT_XML"; // workaround to pass the query type to the server
             this.MedCoparams.psm_query_definition = i2b2.MedCo.QT.query.buildQueryDefinition(qryName);
             this.MedCoparams.psm_result_output = "<result_output_list><result_output priority_index='9' name='patient_count_xml'/>\n</result_output_list>\n";
 
             // callback processor to run the query from definition
             this.MedCocallback = new i2b2_scopedCallback();
             this.MedCocallback.scope = this;
             this.MedCocallback.callback = function (results) {
                 var endTime = new Date().getTime();
                 var duration = endTime-startTime;
                 queryTimes.push(duration);
 
                 numResponses++;
                 // extract the server times
                 try{
                     if (results.error) {
                         alert(results.errorMsg);
                         return;
                     } else {
                         i2b2.MedCo.test.ctrlr.response =  results;
                     }
                 } catch(e){
                     alert("Error when extracting the results of the query: " + e.message)
                 }
 
                 if (numResponses==1){
                     // first query
                     document.getElementById("MedCoTest-QueriesTime").innerHTML = "[" + prettyTime(duration);
                 }
                 else{
                     document.getElementById("MedCoTest-QueriesTime").innerHTML += ", " + prettyTime(duration);
                 }
 
                 if (numResponses < numQueries){
                     // other queries to be sent
                     sendQuery();
                 }
                 else{
                     document.getElementById("MedCoTest-QueriesTime").innerHTML += "]";
                 }
             };
             i2b2.CRC.ajax.runQueryInstance_fromQueryDefinition("PLUGIN:MedCo", this.MedCoparams, this.MedCocallback);
         }
 
         sendQuery();
 
         document.getElementById("MedCoTest-QueryTimeMean").innerHTML = "-";
         document.getElementById("MedCoTest-QueryTimeStd").innerHTML = "-";
 
         // show tot response count
         document.getElementById("MedCoTest-QueryTot").innerHTML = numQueries;
 
         // start timer
         var dothis = function(){
             document.getElementById("MedCoTest-QueryCurr").innerHTML = numResponses;
         };
         var done = function(){
             if (numResponses >= numQueries){
                 // done sending queries. clear panels
                 i2b2.MedCo.QT.ctrlr.clear();
 
                 // compute mean time
                 var mean = 0;
                 for (i=0; i<queryTimes.length; i++){
                     mean += queryTimes[i];
                 }
                 mean /= queryTimes.length;
 
                 // compute std
                 var std = 0;
                 if (queryTimes.length > 1){
                     for (i=0; i<queryTimes.length; i++){
                         std += Math.pow(queryTimes[i]-mean, 2);
                     }
                     std /= queryTimes.length-1;
                     std = Math.sqrt(std);
                 }
 
                 // alert("Query times:" + queryTimes);
                 document.getElementById("MedCoTest-QueryTimeMean").innerHTML = prettyTime(mean);
                 document.getElementById("MedCoTest-QueryTimeStd").innerHTML = prettyTime(std);
                 return true
             }
             return false
         };
         this.startTimer(startTime, "MedCoTest-QueryTime", done, dothis);
     },
 
     decrypt: function(){
         if (this.doing != ""){
             alert("Already " + this.doing);
             return
         }
         if (!this.response){
             alert("No response to be decrypted.");
             return
         }
         this.doing = "decrypting...";
 
         // clear decryption cache and start decryption
         i2b2.MedCo.ctrlr.background.decryptionCache = {};
 
         var startTime = new Date().getTime();
 
         i2b2.MedCo.QT.query.showResponse(this.response, "MedCoTest-QueryResult");
 
         // show number of patient counts to be decrypted and start timer
         var tot = this.response.refXML.getElementsByTagName('query_result_instance').length;
         document.getElementById("MedCoTest-DecryptTot").innerHTML = tot;
         document.getElementById("MedCoTest-DecryptCurr").innerHTML = 0;
 
         var dothis = function(){
             document.getElementById("MedCoTest-DecryptCurr").innerHTML = tot - i2b2.MedCo.ctrlr.background.remainingToDecrypt;
         };
         this.startTimer(startTime, "MedCoTest-DecryptTime", i2b2.MedCo.ctrlr.background.decryptionDone, dothis);
     },
 
     getSelectedQuery: function(){
         switch(document.getElementById('MedCoTest-QueryType').value) {
             case "A":
                 return this.queryA;
                 break;
             case "B":
                 return this.queryB;
                 break;
             case "B_noPTEN":
                 return this.queryB_noPTEN;
                 break;
             case "S1":
                 return this.queryTest1;
             case "S2":
                 return this.queryTest2;
             default:
                 alert("Query type not recognized.")
                 return
         }
     },
 
     getNumQueries: function(){
         return parseInt(document.getElementById('MedCoTest-NumQueries').value)
     },
 
     queryChanged: function(){
         this.encrypted = false;
         switch(document.getElementById('MedCoTest-QueryType').value){
             case "A":
                 document.getElementById("MedCoTest-QueryDescr").innerHTML = "Cutaneous Melanoma AND gene braf AND (protein change V600E OR V600K)";
                 break;
             case "B":
                 document.getElementById("MedCoTest-QueryDescr").innerHTML = "Cutaneous Melanoma AND gene braf AND (genes pten OR cdkn2a OR map2k1 OR mpa2k2)";
                 break;
             case "B_noPTEN":
                 document.getElementById("MedCoTest-QueryDescr").innerHTML = "Cutaneous Melanoma AND gene braf AND (genes cdkn2a OR map2k1 OR mpa2k2)";
                 break;
             case "S1":
                 document.getElementById("MedCoTest-QueryDescr").innerHTML = "Tumor Tissue Site\\Adrenal (non sensitive)";
                 break;
             case "S2":
                 document.getElementById("MedCoTest-QueryDescr").innerHTML = "Cutaneous Melanoma (sensitive)";
                 break;
 
         }
     },
 
     startTimer: function(startTime, label, stop, dothis){
         // label: id of the html object in which write the time
         // stop: function which returns a boolean (true if the action has been completed => stop the timer)
         // dothis: if given this function is while updating the timer
         this.clearTimer();
         this.startTime = startTime;
         this.timeinterval = setInterval(function(){i2b2.MedCo.test.ctrlr.updateTimer(label, stop, dothis)}, 100);
     },
 
     updateTimer: function(label, stop, dothis){
         if (dothis instanceof Function) {
             dothis();
         }
         var now = new Date().getTime();
         document.getElementById(label).innerHTML = prettyTime(now-this.startTime);
         if (stop()){
             this.stopTimer()
         }
     },
 
     clearTimer: function(){
         this.startTime = null;
         clearInterval(this.timeinterval);
         this.timeinterval = null;
     },
 
     stopTimer: function(){
         this.clearTimer();
         this.doing = "";
     },
 
     defineQuery: function(query){
         // given a query, build it from description. Returns false if we are missing some parameters (variant ids).
 
         // clone the description
         query.definition = JSON.parse(JSON.stringify(query.description));
         // for every panel
         for (var panel=0; panel< query.definition.length; panel++){
             // for every "row" in the panel
             for (var parameter=0; parameter<query.definition[panel].length; parameter++) {
                 if (query.definition[panel][parameter].values.name in this.parameter_to_values) {
                     query.definition[panel][parameter].values =
                         this.parameter_to_values[query.definition[panel][parameter].values.name]
                 }
                 else{
                     query.definition = null;
                     return false
                 }
             }
         }
         return true
     }
 };
 
 function prettyTime(milliseconds){
     return (milliseconds/1000).toFixed(2)
 }
\ No newline at end of file