diff --git a/js-i2b2/cells/plugins/MedCo/MedCo_ctrlr.js b/js-i2b2/cells/plugins/MedCo/MedCo_ctrlr.js
index 49f2f56..913d3ab 100644
--- a/js-i2b2/cells/plugins/MedCo/MedCo_ctrlr.js
+++ b/js-i2b2/cells/plugins/MedCo/MedCo_ctrlr.js
@@ -1,322 +1,324 @@
/***********************
* @ProjectDescription Secure count query for sensitive genomic and clinical data with strong privacy guarantees.
* @inherits i2b2
* @namespace i2b2.MedCo
* @author LCA1 EPFL
* @version 0.1
* --------------------------------------------------------------------------------------------------------------------
* This plugin is based on Tutorial plugin and examples on the webclient plugin development guide.
*/
i2b2.MedCo.Init = function(loadedDiv) {
// setup model variables for this plugin
// i2b2.MedCo.model.responseXML = '';
// i2b2.MedCo.model.responseString = '';
// i2b2.MedCo.model.requestQuery = '';
// i2b2.MedCo.model.requestPSet = '';
// i2b2.MedCo.model.requestQueryType = '';
// i2b2.MedCo.model.requestQueryName = '';
// i2b2.MedCo.model.prsRecord = undefined;
// i2b2.MedCo.model.infoType = true;
// i2b2.MedCo.model.varType = true;
// i2b2.MedCo.view.tabId = 0;
// set drag and drop
// i2b2.sdx.Master.AttachType("medco-pset", "PRS", {dropTarget: true});
// i2b2.sdx.Master.setHandlerCustom("medco-pset", "PRS", "DropHandler", i2b2.MedCo.ctrlr.prsDropped);
// register handlers for the medco query tool panels
var panels = ["medcoQryToolPanel1", "medcoQryToolPanel2", "medcoQryToolPanel3"];
var eventRouterFunc =
[
function (sdxData) {i2b2.MedCo.doDrop(sdxData, 0);},
function (sdxData) {i2b2.MedCo.doDrop(sdxData, 1);},
function (sdxData) {i2b2.MedCo.doDrop(sdxData, 2);}];
for (var i = 0; i < panels.length; i++) {
var op_trgt = {dropTarget: true};
i2b2.sdx.Master.AttachType(panels[i], 'CONCPT', op_trgt);
// i2b2.sdx.Master.AttachType(panels[i], 'QM', op_trgt);
// i2b2.sdx.Master.AttachType(panels[i], 'QI', op_trgt);
// i2b2.sdx.Master.AttachType(panels[i], 'PRS', op_trgt);
// i2b2.sdx.Master.AttachType(panels[i], 'PRC', op_trgt);
// i2b2.sdx.Master.AttachType(panels[i], 'PR', op_trgt);
// i2b2.sdx.Master.AttachType(panels[i], 'QDEF', op_trgt);
// i2b2.sdx.Master.AttachType(panels[i], 'QGDEF', op_trgt);
// i2b2.sdx.Master.AttachType(panels[i], 'XML', op_trgt);
// register drop event handler
i2b2.sdx.Master.setHandlerCustom(panels[i], 'CONCPT', 'DropHandler', eventRouterFunc[i]);
// i2b2.sdx.Master.setHandlerCustom(panels[i], 'QM', 'DropHandler', eventRouterFunc[i]);
// i2b2.sdx.Master.setHandlerCustom(panels[i], 'QI', 'DropHandler', eventRouterFunc[i]);
// i2b2.sdx.Master.setHandlerCustom(panels[i], 'PRS', 'DropHandler', eventRouterFunc[i]);
// i2b2.sdx.Master.setHandlerCustom(panels[i], 'PRC', 'DropHandler', eventRouterFunc[i]);
// i2b2.sdx.Master.setHandlerCustom(panels[i], 'PR', 'DropHandler', eventRouterFunc[i]);
// i2b2.sdx.Master.setHandlerCustom(panels[i], 'QDEF', 'DropHandler', eventRouterFunc[i]);
// i2b2.sdx.Master.setHandlerCustom(panels[i], 'QGDEF', 'DropHandler', eventRouterFunc[i]);
// i2b2.sdx.Master.setHandlerCustom(panels[i], 'XML', 'DropHandler', eventRouterFunc[i]);
}
// manage YUI tabs
i2b2.MedCo.view.yuiTabs = new YAHOO.widget.TabView("MedCo-TABS", {activeIndex: 0});
// put in an array all the (three) panels for easier access
i2b2.MedCo.view.panels = document.getElementsByClassName("medcoQryToolPanel");
for (var i = 0 ; i < 3; i++){
i2b2.MedCo.view.panels[i].innerHTML = ""
}
// initialize empty parameter for the query (no panels content)
i2b2.MedCo.model.panels = [[], [], []]; // three panels
// POPUP init
- // i2b2.MedCo.ctrlr.PopupInit();
+ // i2b2.MedCo.ctrlr.PopupInit(); todo delete (old popup initialization)
- // GENE POPUP
+ // POPUPS
i2b2.MedCo.ctrlr.genePopup.init();
+ i2b2.MedCo.ctrlr.variantNamePopup.init();
+
// store how many responses I am waiting for (I have to wait to receive all the variants before sending the query)
i2b2.MedCo.ctrlr.variantsQueryCounter = 0;
};
i2b2.MedCo.Unload = function() {
// purge old data
i2b2.MedCo.model = {};
i2b2.MedCo.view = {};
return true;
};
i2b2.MedCo.doDrop = function(sdxData, nPanel) {
sdxData = sdxData[0]; // only interested in first record
// save the info to our local data model
i2b2.MedCo.model.panels[nPanel].push(sdxData);
// show the info to the user
i2b2.MedCo.view.panels[nPanel].innerHTML += sdxData.sdxInfo.sdxDisplayName + "<br>";
// CHECK: some usefull 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;
// TODO if is "Genomic annotations" then open a popup to insert the annotations
if (sdxData.sdxInfo.sdxDisplayName == "Laboratory Tests"){
i2b2.MedCo.popupShow(nPanel);
};
};
i2b2.MedCo.ctrlr.clear = function(){
for (i = 0; i < i2b2.MedCo.view.panels.length; i++){
i2b2.MedCo.view.panels[i].innerHTML = "";
};
i2b2.MedCo.model.panels = [[], [], []];
};
i2b2.MedCo.ctrlr.run = function(){
// show the loading gif
document.getElementById("MED-plainResult").innerHTML = "<img id=\"MED-loadingGif\" width=\"20px\" src=\"assets/images/spin.gif\">";
document.getElementById("MED-loadingGif").style.display = 'block';
// wait until you receive all the variants you requested
while (i2b2.MedCo.popup.variantsQueryCounter != 0) {
// try again later to run the query
setTimeout(i2b2.MedCo.ctrlr.run, 500);
return
}
// todo delete. just checking the variables correspond with the ones in the panels
// for (var i = 0; i<3; i++){
// alert(i2b2.MedCo.model.panels[i].map(function(e) {
// if (typeof e === 'object'){
// return e.sdxInfo.sdxDisplayName
// }else{
// return e
// }
// }
// )
// );
// }
// callback processor to run the query from definition
this.MedCocallback = new i2b2_scopedCallback();
this.MedCocallback.scope = this;
this.MedCocallback.callback = function(results) {
try{
// alert("full message" + JSON.stringify(results));
if (results.error) {
alert(results.errorMsg);
return;
} else {
// // "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]
// alert("response" + JSON.stringify(results.msgResponse));
// hide the loading gif
document.getElementById("MED-loadingGif").style.display = 'none';
// show the patient count
var qi_list = results.refXML.getElementsByTagName('query_result_instance');
patientCount = i2b2.h.getXNodeVal(qi_list[0], 'set_size');
document.getElementById("MED-plainResult").innerHTML = patientCount;
}
} catch(e){
alert("exception")
}
};
this.MedCoparams = {};
this.MedCoparams.result_wait_time = 180;
this.MedCoparams.psm_query_definition = i2b2.MedCo.ctrlr.QueryDefinition("MedCo_query"); // chose a name for the query
// show the query
logdiv = document.getElementById("mylog");
logdiv.innerHTML= i2b2.h.Escape(this.MedCoparams.psm_query_definition);
this.MedCoparams.psm_result_output = i2b2.MedCo.ctrlr.ResultOutput;
i2b2.CRC.ajax.runQueryInstance_fromQueryDefinition("PLUGIN:MedCo", this.MedCoparams, this.MedCocallback);
};
i2b2.MedCo.ctrlr.ResultOutput = "<result_output_list><result_output priority_index=\"9\" name=\"patient_count_xml\"/>\n</result_output_list>\n";
// return the query xml
i2b2.MedCo.ctrlr.QueryDefinition = function (name){
//"<query_definition>\n\t<query_name>undefined</query_name>\n\t<query_timing>ANY</query_timing>\n\t<specificity_scale>0</specificity_scale>\n\t<panel>\n\t\t<panel_number>1</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t<item>\n\t\t\t<hlevel>1</hlevel>\n\t\t\t<item_name>Procedures</item_name>\n\t\t\t<item_key>\\\\i2b2_PROC\\i2b2\\Procedures\\</item_key>\n\t\t\t<tooltip>Procedures</tooltip>\n\t\t\t<class>ENC</class>\n\t\t\t<item_icon>FA</item_icon>\n\t\t\t<item_is_synonym>false</item_is_synonym>\n\t\t</item>\n\t</panel>\n</query_definition>\n"
// get the time of the query
var d = new Date();
var time = d.getHours().toString() + ":" + d.getMinutes().toString() + ":" + d.getSeconds().toString();
var queryxml = "<query_definition>\n\t<query_name>" + name + "@" + time + "</query_name>\n\t<query_timing>ANY</query_timing>\n\t<specificity_scale>0</specificity_scale>\n\t";
// hardcoded query1 (result should be 102)
// queryxml += "<panel>\n\t\t<panel_number>1</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t<item>\n\t\t\t<hlevel>1</hlevel>\n\t\t\t<item_name>Procedures</item_name>\n\t\t\t<item_key>\\\\i2b2_PROC\\i2b2\\Procedures\\</item_key>\n\t\t\t<tooltip>Procedures</tooltip>\n\t\t\t<class>ENC</class>\n\t\t\t<item_icon>FA</item_icon>\n\t\t\t<item_is_synonym>false</item_is_synonym>\n\t\t</item>\n\t</panel>";
// hardcoded query2 (result should be 36)
// queryxml += "<panel>\n\t\t<panel_number>1</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t<item>\n\t\t\t<hlevel>2</hlevel>\n\t\t\t<item_name>Circulatory system</item_name>\n\t\t\t<item_key>\\\\i2b2_DIAG\\i2b2\\Diagnoses\\Circulatory system (390-459)\\</item_key>\n\t\t\t<tooltip>Diagnoses \\ Circulatory system</tooltip>\n\t\t\t<class>ENC</class>\n\t\t\t<item_icon>FA</item_icon>\n\t\t\t<item_is_synonym>false</item_is_synonym>\n\t\t</item>\n\t</panel>\n\t";
// queryxml += "<panel>\n\t\t<panel_number>2</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t<item>\n\t\t\t<hlevel>2</hlevel>\n\t\t\t<item_name>Affymetrix HG-U133</item_name>\n\t\t\t<item_key>\\\\i2b2_EXPR\\i2b2\\Expression Profiles Data\\Affymetrix HG-U133\\</item_key>\n\t\t\t<tooltip>Expression Profiles Data\\Affymetrix HG-U133</tooltip>\n\t\t\t<class>ENC</class>\n\t\t\t<item_icon>FA</item_icon>\n\t\t\t<item_is_synonym>false</item_is_synonym>\n\t\t</item>\n\t\t<item>\n\t\t\t<hlevel>2</hlevel>\n\t\t\t<item_name>Skin diseases</item_name>\n\t\t\t<item_key>\\\\i2b2_DIAG\\i2b2\\Diagnoses\\Skin diseases (680-709)\\</item_key>\n\t\t\t<tooltip>Diagnoses \\ Skin diseases</tooltip>\n\t\t\t<class>ENC</class>\n\t\t\t<item_icon>FA</item_icon>\n\t\t\t<item_is_synonym>false</item_is_synonym>\n\t\t</item>\n\t</panel>\n\t";
// queryxml += "<panel>\n\t\t<panel_number>3</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t<item>\n\t\t\t<hlevel>3</hlevel>\n\t\t\t<item_name>Diagnostic and nonsurgical procedures</item_name>\n\t\t\t<item_key>\\\\i2b2_PROC\\i2b2\\Procedures\\PRC\\ICD9 (Inpatient)\\(87-99) Diagnostic and nonsurgical procedures\\</item_key>\n\t\t\t<tooltip>Procedures \\ ICD9 (Inpatient) \\ Diagnostic and nonsurgical procedures</tooltip>\n\t\t\t<class>ENC</class>\n\t\t\t<item_icon>FA</item_icon>\n\t\t\t<item_is_synonym>false</item_is_synonym>\n\t\t</item>\n\t</panel>\n"
// hardcoded query2 it run even if there is only the key for the concepts
// queryxml += "<panel>\n\t\t<panel_number>1</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t<item>\n\t\t\t<item_key>\\\\i2b2_DIAG\\i2b2\\Diagnoses\\Circulatory system (390-459)\\</item_key>\n\t\t</item>\n\t</panel>\n\t";
// queryxml += "<panel>\n\t\t<panel_number>2</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t<item>\n\t\t\t<item_key>\\\\i2b2_EXPR\\i2b2\\Expression Profiles Data\\Affymetrix HG-U133\\</item_key>\n\t\t</item>\n\t\t<item>\n\t\t\t<item_key>\\\\i2b2_DIAG\\i2b2\\Diagnoses\\Skin diseases (680-709)\\</item_key>\n\t\t</item>\n\t</panel>\n\t";
// queryxml += "<panel>\n\t\t<panel_number>3</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t<item>\n\t\t\t<item_key>\\\\i2b2_PROC\\i2b2\\Procedures\\PRC\\ICD9 (Inpatient)\\(87-99) Diagnostic and nonsurgical procedures\\</item_key>\n\t\t</item>\n\t</panel>\n"
for (i = 0 ; i < 3; i++){ // there are 3 panels
params = i2b2.MedCo.model.panels[i];
nparams = params.length;
if (nparams != 0) { // 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 += "<panel>\n\t\t<panel_number>" + i + "</panel_number>\n\t\t<panel_accuracy_scale>100</panel_accuracy_scale>\n\t\t<invert>0</invert>\n\t\t<panel_timing>ANY</panel_timing>\n\t\t<total_item_occurrences>1</total_item_occurrences>\n\t\t";
for (j = 0; j < nparams; j++){
// inters an item object for every concept
queryxml += "\t\t<item>\n";
sdxData = params[j];
switch(sdxData.sdxInfo.sdxType) { // copied from js-i2b2/cells/CRC/CRC_ctrlr_QryTool.js
case "QM":
if(sdxData.origData.id.startsWith("masterid")) // BUG FIX: WEBCLIENT-149
queryxml += '\t\t\t<item_key>' + sdxData.origData.id + '</item_key>\n';
else
queryxml += '\t\t\t<item_key>masterid:' + sdxData.origData.id + '</item_key>\n';
queryxml += '\t\t\t<item_name>' + i2b2.h.Escape(sdxData.origData.title) + '</item_name>\n';
queryxml += '\t\t\t<tooltip>' + i2b2.h.Escape(sdxData.origData.name) + '</tooltip>\n';
queryxml += '\t\t\t<item_is_synonym>false</item_is_synonym>\n';
queryxml += '\t\t\t<hlevel>0</hlevel>\n';
break;
case "PRS":
queryxml += '\t\t\t<item_key>patient_set_coll_id:' + sdxData.sdxInfo.sdxKeyValue + '</item_key>\n';
queryxml += '\t\t\t<item_name>' + i2b2.h.Escape(sdxData.sdxInfo.sdxDisplayName) + '</item_name>\n';
queryxml += '\t\t\t<tooltip>' + i2b2.h.Escape(sdxData.sdxInfo.sdxDisplayName) + '</tooltip>\n';
queryxml += '\t\t\t<item_is_synonym>false</item_is_synonym>\n';
queryxml += '\t\t\t<hlevel>0</hlevel>\n';
break;
case "ENS":
queryxml += '\t\t\t<item_key>patient_set_enc_id:' + sdxData.sdxInfo.sdxKeyValue + '</item_key>\n';
queryxml += '\t\t\t<item_name>' + i2b2.h.Escape(sdxData.sdxInfo.sdxDisplayName) + '</item_name>\n';
queryxml += '\t\t\t<tooltip>' + i2b2.h.Escape(sdxData.sdxInfo.sdxDisplayName) + '</tooltip>\n';
queryxml += '\t\t\t<item_is_synonym>false</item_is_synonym>\n';
queryxml += '\t\t\t<hlevel>0</hlevel>\n';
break;
default:
if (sdxData.origData.isModifier) {
var modParent = sdxData.origData.parent;
var level = sdxData.origData.level;
var key = sdxData.origData.parent.key;
var name = (sdxData.origData.parent.name != null ? i2b2.h.Escape(sdxData.origData.parent.name) : i2b2.h.Escape(sdxData.origData.name)) ;
var tooltip = sdxData.origData.tooltip;
var itemicon = sdxData.origData.hasChildren;
while (modParent != null)
{
if (modParent.isModifier)
{
modParent = modParent.parent;
} else {
level = modParent.level;
key = modParent.key;
name = modParent.name;
tooltip = modParent.tooltip;
itemicon = modParent.hasChildren;
break;
}
}
// queryxml += '\t\t\t<hlevel>' + level + '</hlevel>\n';
queryxml += '\t\t\t<item_key>' + key + '</item_key>\n';
// queryxml += '\t\t\t<item_name>' + i2b2.h.Escape(name) + '</item_name>\n';
// // (sdxData.origData.newName != null ? sdxData.origData.newName : sdxData.origData.name) + '</item_name>\n';
// queryxml += '\t\t\t<tooltip>' + i2b2.h.Escape(tooltip) + '</tooltip>\n';
// queryxml += '\t\t\t<item_icon>' + itemicon + '</item_icon>\n';
// queryxml += '\t\t\t<class>ENC</class>\n';
queryxml += '\t\t\t\t<constrain_by_modifier>\n';
queryxml += '\t\t\t\t\t<modifier_name>' + sdxData.origData.name + '</modifier_name>\n';
queryxml += '\t\t\t\t\t<applied_path>' + sdxData.origData.applied_path + '</applied_path>\n';
queryxml += '\t\t\t\t\t<modifier_key>' + sdxData.origData.key + '</modifier_key>\n';
if (sdxData.ModValues)
{
queryxml += i2b2.CRC.view.modLabvaluesCtlr.getModLabValuesForXML(sdxData.ModValues);
}
queryxml += '\t\t\t\t</constrain_by_modifier>\n';
} else {
sdxData.origData.key = (sdxData.origData.key).replace(/</g,"<");
// sdxData.origData.name = (sdxData.origData.name).replace(/</g,"<");
// if (undefined != sdxData.origData.tooltip)
// sdxData.origData.tooltip = (sdxData.origData.tooltip).replace(/</g,"<");
// queryxml += '\t\t\t<hlevel>' + sdxData.origData.level + '</hlevel>\n';
// //s += '\t\t\t<item_name>' + (sdxData.origData.newName != null ? i2b2.h.Escape(sdxData.origData.newName) : i2b2.h.Escape(sdxData.origData.name)) + '</item_name>\n';
// queryxml += '\t\t\t<item_name>' + (sdxData.origData.name != null ? i2b2.h.Escape(sdxData.origData.name) : i2b2.h.Escape(sdxData.origData.newName)) + '</item_name>\n';
queryxml += '\t\t\t<item_key>' + sdxData.origData.key + '</item_key>\n';
// queryxml += '\t\t\t<tooltip>' + i2b2.h.Escape(sdxData.origData.tooltip) + '</tooltip>\n'; // BUG FIX: WEBCLIENT-135 (Escape tooltip)
// queryxml += '\t\t\t<class>ENC</class>\n';
// queryxml += '\t\t\t<item_icon>' + sdxData.origData.hasChildren + '</item_icon>\n';
}
try {
var t = i2b2.h.XPath(sdxData.origData.xmlOrig,'descendant::synonym_cd/text()');
t = (t[0].nodeValue=="Y");
} catch(e) {
var t = "false";
}
queryxml += '\t\t\t<item_is_synonym>'+t+'</item_is_synonym>\n';
if (sdxData.LabValues && !jQuery.isEmptyObject(sdxData.LabValues)) {
queryxml += i2b2.CRC.view.modLabvaluesCtlr.getModLabValuesForXML(sdxData.LabValues);
}
break;
}
queryxml += '\t\t</item>\n';
}
queryxml +="\n\t</panel>\n"
}
}
queryxml += "\n</query_definition>\n";
return queryxml
};
function backslashX2(str) {
return str.replace("\\", "\\\\");
}
// whole harcoded query, should return 13
// <query_definition> <query_name>query3@9:47:2</query_name> <query_timing>ANY</query_timing> <specificity_scale>0</specificity_scale> <panel> <panel_number>0</panel_number> <panel_accuracy_scale>100</panel_accuracy_scale> <invert>0</invert> <panel_timing>ANY</panel_timing> <total_item_occurrences>1</total_item_occurrences> <item> <item_key>\\i2b2_PROC\i2b2\Procedures\PRC\ICD9 (Inpatient)\(87-99) Diagnostic and nonsurgical procedures\</item_key> <item_is_synonym>false</item_is_synonym> </item> </panel> <panel> <panel_number>1</panel_number> <panel_accuracy_scale>100</panel_accuracy_scale> <invert>0</invert> <panel_timing>ANY</panel_timing> <total_item_occurrences>1</total_item_occurrences> <item> <item_key>\\i2b2_PROV\i2b2\Providers\Emergency\</item_key> <item_is_synonym>false</item_is_synonym> </item> </panel> </query_definition>
\ No newline at end of file
diff --git a/js-i2b2/cells/plugins/MedCo/assets/injected_screens.html b/js-i2b2/cells/plugins/MedCo/assets/injected_screens.html
index d761012..b2f8a7e 100644
--- a/js-i2b2/cells/plugins/MedCo/assets/injected_screens.html
+++ b/js-i2b2/cells/plugins/MedCo/assets/injected_screens.html
@@ -1,239 +1,254 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html>
<body>
<div id='MedCo-mainDiv'>
<div id="MedCo-TABS" class="yui-navset">
<!--tabs definitions-->
<ul class="yui-nav">
<li id="MedCo-TAB0" class="selected"><a href="#MedCo-TAB0"><em>Secure Query Dashboard</em></a></li>
<!--<li id="MedCo-TAB1"><a href="#MedCo-TAB1"><em>Genomic Annotations Attributes</em></a></li>-->
<!--<li id="MedCo-TAB2"><a href="#MedCo-TAB2"><em>Clinical Ontology Attributes</em></a></li>-->
<li id="MedCo-TAB3"><a href="#MedCo-TAB3"><em>Plugin Help</em></a></li>
</ul>
<!-- tabs definition -->
<div class="yui-content" id="MedCo-CONTENT">
<!-- Secure Query DashBoard tab -->
<div class="MedCo-Dashboard">
<!-- run - reset - drop patient set - query for query status - decrypt result -->
<div class="MedCo-ControlButtons">
- <!-- Popup -->
- <div id="annoMessage" class="popupMessage">
- <div>
- <h1>Annotations</h1>
- <div style="margin: 5px 10px 10px 10px">
- <label>
- Select an annotation:
- <input type="search" id="searchAnnotationBox">
- <select id="annotationList" onchange="i2b2.MedCo.ctrlr.loadAnnotationValues()">
-
- </select>
- </label>
-
- <br>
-
- <label>
- Select a value:
- <input type="search" id="searchAnnotationValueBox">
- <!--<div id="MED-loadingValues" style="float:left;"></div>-->
- <!--todo often too many values (20 000) the select is useless and slow-->
- <!--<select id="annotationValueList">-->
+ <!-- old popup todo delete <!– Popup –>-->
+ <!--<div id="annoMessage" class="popupMessage">-->
+ <!--<div>-->
+ <!--<h1>Annotations</h1>-->
+ <!--<div style="margin: 5px 10px 10px 10px">-->
+ <!--<label>-->
+ <!--Select an annotation:-->
+ <!--<input type="search" id="searchAnnotationBox">-->
+ <!--<select id="annotationList" onchange="i2b2.MedCo.ctrlr.loadAnnotationValues()">-->
<!--</select>-->
-
- <!--use span for inline text-->
- <span id="selectedAnnotationValue"></span>
- </label>
+ <!--</label>-->
<!--<br>-->
- <!--a textbox to write down annotations-->
<!--<label>-->
- <!--Write the annotations separated by a ';':-->
- <!--<input-->
- <!--id="written_annotations"-->
- <!--type="text"-->
- <!--value="annotation x"-->
- <!--onkeypress="i2b2.MedCo.popupEnterPressed(event)">-->
+ <!--Select a value:-->
+ <!--<input type="search" id="searchAnnotationValueBox">-->
+ <!--<!–<div id="MED-loadingValues" style="float:left;"></div>–>-->
+ <!--<!–todo often too many values (20 000) the select is useless and slow–>-->
+ <!--<!–<select id="annotationValueList">–>-->
+
+ <!--<!–</select>–>-->
+
+ <!--<!–use span for inline text–>-->
+ <!--<span id="selectedAnnotationValue"></span>-->
<!--</label>-->
- <div>
- <input type="button" value="Ok" onclick="i2b2.MedCo.popupOk()" style="float: left">
- <input type="button" value="Cancel" onclick="i2b2.MedCo.popupHide()" style="float: right">
- </div>
- </div>
+ <!--<!–<br>–>-->
+
+ <!--<!–a textbox to write down annotations–>-->
+ <!--<!–<label>–>-->
+ <!--<!–Write the annotations separated by a ';':–>-->
+ <!--<!–<input–>-->
+ <!--<!–id="written_annotations"–>-->
+ <!--<!–type="text"–>-->
+ <!--<!–value="annotation x"–>-->
+ <!--<!–onkeypress="i2b2.MedCo.popupEnterPressed(event)">–>-->
+ <!--<!–</label>–>-->
+
+ <!--<div>-->
+ <!--<input type="button" value="Ok" onclick="i2b2.MedCo.popupOk()" style="float: left">-->
+ <!--<input type="button" value="Cancel" onclick="i2b2.MedCo.popupHide()" style="float: right">-->
+ <!--</div>-->
+ <!--</div>-->
- </div>
- </div>
- <!-- -->
-
- <input type="button" onclick="i2b2.MedCo.ctrlr.genePopup.show(1);" value="show"/>
-
- <!-- popup2 -->
- <div id="MedCo_genePopup" style="display:none;">
- <div class="hd">Search by Gene</div>
- <div class="bd" id="modifier-viewer-body1">
- <p>
- Use the gene name box to specify the variant for which to search. When you
- begin typing in the search box below, a dropdown list will appear after you
- type the first characters.
- </p>
-
- <table class="MedCo_popupTable">
- <tr>
- <th> Gene Name* </th>
- <td>
- <input type="search" id="searchGeneInputBox">
- </td>
- <td>
- <!-- todo I should update too when the user clicks the already selected option -->
- <select id="geneList" onchange="
- document.querySelector('#searchGeneInputBox').value = this.options[this.selectedIndex].text;">
- </select>
- </td>
- </tr>
-
- <!--<tr>-->
- <!--<td colspan="3">-->
- <!--<br>-->
- <!--<p>Please note the zygosity options in the dropdown list</p>-->
- <!--</td>-->
- <!--</tr>-->
-
- <tr>
- <th>Zygosity*</th>
- <td>
- <select id="zygosityList">
- <option value="Any">
- Any
- </option>
- <option value="Heterozygous">
- Heterozygous
- </option>
- <option value="Homozygous">
- Homozygous
- </option>
- <option value="Unknown">
- Unknown
- </option>
- </select>
- </td>
- </tr>
- <tr>
- <th>Consequence</th>
- <td> ? </td>
- </tr>
- </table>
- <!--<center>-->
- <!--<input type="submit" value="OK" onClick="alert('OKHTML');">-->
- <!--<input type="submit" value="Cancel" onClick="i2b2.MedCo.ctrlr.genePopup.popup.hide();">-->
- <!--</center>-->
- </div>
- <div class="ft"></div>
- </div>
- <!-- -->
+ <!--</div>-->
+ <!--</div>-->
+ <!--<!– –>-->
+
+ <input type="button" onclick="i2b2.MedCo.ctrlr.genePopup.show(1);" value="show gene popup"/>
+ <input type="button" onclick="i2b2.MedCo.ctrlr.variantNamePopup.show(1);" value="show variant name popup"/>
<h2 class="medcoQryToolTitle">Drop concepts here</h2>
<div class="medcoQryToolPanels">
<div>
<!--<div class="droptrgtlbl">Drop concepts here</div>-->
<div id="medcoQryToolPanel1" class="medcoQryToolPanel droptrgt SDX-PRS">
<p id="panel1content"> </p>
</div>
<div id="medcoQryToolPanel2" class="medcoQryToolPanel droptrgt SDX-PRS">
<p id="panel2content"> </p>
</div>
<div id="medcoQryToolPanel3" class="medcoQryToolPanel droptrgt SDX-PRS">
<p id="panel3content"> </p>
</div>
<!--<!–Show chosen annotations–>-->
<!--<div style="background-color: aliceblue; height: 100%; " class="medcoQryToolPanel">-->
<!--<h3>Chosen annotations: </h3>-->
<!--<p id="chosen_annotations"> </p>-->
<!--<input type="button" value="Clear" onclick="i2b2.MedCo.Clear()">-->
<!--</div>-->
<!--<!– –>-->
</div>
</div>
<div>
<div style="padding-top: 10px">
<div class="MED-Buttons">
<div class="runButton"><a href="JavaScript:i2b2.MedCo.ctrlr.run()">Run Query</a></div>
<div class="resetButton"><a href="JavaScript:i2b2.MedCo.ctrlr.clear()">Clear</a></div>
</div>
<table class="MED-resultTable">
<tbody>
<tr>
<td>Number of patients</td>
</tr>
<tr>
<td id="MED-plainResult">
-
</td>
</tr>
</tbody>
</table>
<!--<div class="statusBox"><a href="JavaScript:i2b2.MedCo.ctrlr.queryStatus()">Query Status</a></div>-->
<!-- status info goes into lower status div in i2b2 -->
</div>
</div>
<div id="mylog" style="overflow: scroll; width: 100%; height: 100%;">
</div>
</div>
</div>
<!-- Genomic Annotations Attributes tab -->
<!--<div>-->
<!--<div id="byGene" style="disply:block;">-->
<!--<div class="label">Genomic Annotations Search</div>-->
<!--<input type="string" name="gene_input" id="gene_input" class="medco-input"/>-->
<!--</div>-->
<!--<div id="annotations_display">-->
<!--<!– dynamically inserted annotations text –>-->
<!--<!– TODO: autocompletion in text bow –>-->
<!--</div>-->
<!--</div>-->
<!-- Clinical Ontology Attributes tab -->
<!--<div>-->
<!--<div id="secure_ontology_selector">-->
<!--<!– dynamically inserted ontology query builder –>-->
<!--</div>-->
<!--</div>-->
<!-- Plugin Help tab -->
<div>
<div class="MedCo-MainContent">
<div class="MedCo-MainContentPad">
</div>
</div>
</div>
+ <!-- gene popup -->
+ <div id="MedCo_genePopup" style="visibility: collapse;">
+ <div class="hd">Search by Gene</div>
+ <div class="bd">
+ <p>
+ Use the gene name box to specify the variant for which to search. When you
+ begin typing in the search box below, the dropdown list will be populated with
+ some matching options. Regular expressions are accepted.
+ </p>
+
+ <table class="MedCo_popupTable">
+ <tr>
+ <th> Gene Name* </th>
+ <td>
+ <input type="search" id="searchGeneInputBox">
+ </td>
+ <td>
+ <!-- todo I should update too when the user clicks the already selected option -->
+ <select id="geneList" onchange="
+ document.querySelector('#searchGeneInputBox').value = this.options[this.selectedIndex].text;">
+ </select>
+ </td>
+ </tr>
+
+ <tr>
+ <th>Zygosity*</th>
+ <td colspan="2">
+ <div id="zygosityListGenePopup">
+ <label><input type="checkbox" id="heterozygousGenePopup">Heterozygous</label>
+ <label><input type="checkbox" id="homozygousGenePopup">Homozygous</label>
+ <label><input type="checkbox" id="unknownGenePopup">Unknown</label>
+ </div>
+ </td>
+ </tr>
+ </table>
+ </div>
+ </div>
+ <!-- -->
+
+ <!-- variant name popup -->
+ <div id="MedCo_variantNamePopup" style="visibility: collapse;">
+ <div class="hd">Search by variant name</div>
+ <div class="bd">
+ <p>
+ Use the variant name box to specify the variant for which to search. When you
+ begin typing in the search box below, the dropdown list will be populated with
+ some matching options. Regular expressions are accepted.
+ </p>
+
+ <table class="MedCo_popupTable">
+ <tr>
+ <th> Variant Name* </th>
+ <td>
+ <input type="search" id="searchVariantNameInputBox">
+ </td>
+ <td>
+ <!-- todo I should update too when the user clicks the already selected option -->
+ <select id="variantNameList" onchange="
+ document.querySelector('#searchGeneInputBox').value = this.options[this.selectedIndex].text;">
+ </select>
+ </td>
+ </tr>
+
+ <tr>
+ <th>Zygosity*</th>
+ <td colspan="2">
+ <div id="zygosityListVariantNamePopup">
+ <label><input type="checkbox" id="heterozygousVariantNamePopup">Heterozygous</label>
+ <label><input type="checkbox" id="homozygousVariantNamePopup">Homozygous</label>
+ <label><input type="checkbox" id="unknownVariantNamePopup">Unknown</label>
+ </div>
+ </td>
+ </tr>
+ </table>
+ </div>
+ </div>
+ <!-- -->
+
</div>
</div>
</div>
</body>
</html>
diff --git a/js-i2b2/cells/plugins/MedCo/assets/vwMedCo.css b/js-i2b2/cells/plugins/MedCo/assets/vwMedCo.css
index afefd25..3509557 100644
--- a/js-i2b2/cells/plugins/MedCo/assets/vwMedCo.css
+++ b/js-i2b2/cells/plugins/MedCo/assets/vwMedCo.css
@@ -1,388 +1,418 @@
/*** CSS for main plugin wrapper ***/
DIV#MedCo-mainDiv {
padding: 0px;
}
/*** CSS for tab background ***/
DIV#MedCo-TABS DIV.yui-content {
background: #FFF;
}
DIV#MedCo-TABS DIV.MedCo-Dashboard {
background:#FFF;
border:solid #63758C;
border-width:1px 0;
overflow:auto;
height:100%;
}
DIV#GEN-TABS DIV.GEN-MainContentPad {
padding:5px 10px;
overflow:hidden;
}
DIV#GEN-TABS DIV.GEN-QueryDefinitionPad {
background:#FFF;
padding:0px 20px;
margin-bottom:30px;
overflow:hidden;
}
DIV#GEN-TABS DIV.GEN-VariantDefinition {
float:left;
overflow:hidden;
}
DIV#GEN-TABS DIV.GEN-Buttons,
DIV#GEN-TABS DIV.GEN-ResultTypes {
padding-left:20px;
margin-bottom:10px;
overflow:hidden;
}
/*** CSS for the Enter Note and View Results tabs ***/
DIV#GEN-TABS .gen-input {
padding: 2px 10px;
background: #DEEBEF;
margin-top: 17px;
margin-bottom: 2px;
text-align:left;
width: 500px;
height: 28px;
border: 1px solid #63758C;
overflow:hidden;
float:left;
}
DIV#GEN-TABS DIV.label {
padding: 8px 0px;
width:80px;
height:16px;
overflow:hidden;
text-align:right;
float: left;
font-weight:bold;
color:#666;
margin: 15px 10px 0px 0px;
}
DIV#GEN-TABS DIV.label2 {
padding: 2px 0px;
width:80px;
height:16px;
overflow:hidden;
text-align:right;
float: left;
font-weight:bold;
color:#666;
margin: 15px 10px 0px 0px;
}
DIV#GEN-TABS DIV.label3 {
width:80px;
height:16px;
overflow:hidden;
text-align:right;
float: left;
font-weight:bold;
color:#666;
padding:0px 20px 5px 0px;
}
DIV#GEN-TABS select.gen-select {
width:200px;
height:20px;
overflow:hidden;
float:left;
background: #DEEBEF;
margin-top: 15px;
border: 1px solid #63758C;
}
DIV#GEN-TABS DIV.radio {
padding: 6px 0px;
width:120px;
height:20px;
overflow:hidden;
text-align:right;
float: left;
font-weight:bold;
color:#666;
margin: 15px 0px 0px 0px;
}
DIV#GEN-TABS DIV.droptrgt {
padding: 5px 10px;
background: #DEEBEF;
margin-top: 15px;
text-align:left;
border: 1px solid #63758C;
width:300px;
overflow:hidden;
white-space:nowrap;
}
DIV#GEN-TABS DIV.dropresult {
padding: 5px 10px;
background: #DEEBEF;
margin-bottom: 15px;
text-align:left;
border: 1px solid #63758C;
width:300px;
overflow:hidden;
white-space:nowrap;
}
DIV#GEN-TABS DIV.closeButton {
opacity:0.5;
background: url('close.gif');
background-size:12px 12px;
background-repeat: no-repeat;
height:12px;
width:12px;
float:right;
margin:2px -2px 0px 4px;
}
DIV#GEN-TABS DIV.loading {
background: url('spin.gif');
background-size:16px 16px;
background-repeat: no-repeat;
height:16px;
width:16px;
margin:0px 5px;
float:left;
}
DIV#GEN-TABS DIV.progress {
margin:0px 0px 10px 0px;
}
DIV#GEN-TABS DIV.resetBox,
DIV#GEN-TABS DIV.runBox {
position:relative;
xdisplay:none;
background:#6677AA;
border:1px solid #667788;
color:#FFFFFF;
font-weight:bold;
font-family:arial,helvetica;
font-size:11px;
height:16px;
line-height:16px;
text-align:center;
color:#FFF;
cursor:pointer;
float: left;
margin:0px 5px 0px 0px;
width:72px;
xz-index:5;
overflow:hidden;
}
DIV#GEN-TABS DIV.resetBox a,
DIV#GEN-TABS DIV.runBox a {
color:#FFF;
display:block;
text-decoration:none;
}
DIV#GEN-TABS DIV.resetBox a:hover,
DIV#GEN-TABS DIV.runBox a:hover {
background-color:#7687bf;
}
/*** CSS for the Plugin Help tab ***/
DIV#GEN-TABS H1 {
margin:0 0 10px 0;
font-size:16px;
color:#42558C;
font-weight:bold;
}
DIV#GEN-TABS H2 {
margin:10px 0 10px 0;
font-size:13px;
color:#42558C;
font-weight:bold;
}
DIV#GEN-TABS HR {
margin:0;
}
-/*Added 11/09/2017*/
+/*!*Added 11/09/2017*!*/
+
+/*!*Popup*!*/
+/*.popupBackground {*/
+ /*display: none;*/
+ /*opacity: .75;*/
+ /*filter: alpha(opacity=75);*/
+ /*-ms-filter: "alpha(opacity=75)";*/
+ /*-khtml-opacity: .75;*/
+ /*-moz-opacity: .75;*/
+ /*background: #B8B8B8;*/
+ /*position: absolute;*/
+ /*left: 0px;*/
+ /*top: 0px;*/
+ /*height: 100%;*/
+ /*width: 100%;*/
+ /*z-index:990*/
+/*}*/
-/*Popup*/
-.popupBackground {
- display: none;
- opacity: .75;
- filter: alpha(opacity=75);
- -ms-filter: "alpha(opacity=75)";
- -khtml-opacity: .75;
- -moz-opacity: .75;
- background: #B8B8B8;
- position: absolute;
- left: 0px;
- top: 0px;
- height: 100%;
- width: 100%;
- z-index:990
-}
-
-.popupMessage {
- display: none;
- position: absolute;
- left: 50%;
- top: 50%;
- /*height: 250px;*/
- /*width: 550px;*/
- /*margin-top should be half of the height*/
- margin-top: -125px;
- /*margin-left should be half of the width*/
- margin-left: -275px;
- background: #BBCCEE;
- border: 1px solid #ccc;
- box-shadow: 3px 3px 7px #777;
- -webkit-box-shadow: 3px 3px 7px #777;
- -moz-border-radius: 5px;
- -webkit-border-radius: 5px;
- z-index:999
-}
-
-.popupMessage h1{
- text-align:center;
- background:#6677AA;
- border:1px solid #314763;
- color:#FFFFFF !important;
- font-size:11px;
- font-weight:bold;
- height:13px;
- line-height:12px;
- padding: 5px;
-}
+/*.popupMessage {*/
+ /*display: none;*/
+ /*position: absolute;*/
+ /*left: 50%;*/
+ /*top: 50%;*/
+ /*!*height: 250px;*!*/
+ /*!*width: 550px;*!*/
+ /*!*margin-top should be half of the height*!*/
+ /*margin-top: -125px;*/
+ /*!*margin-left should be half of the width*!*/
+ /*margin-left: -275px;*/
+ /*background: #BBCCEE;*/
+ /*border: 1px solid #ccc;*/
+ /*box-shadow: 3px 3px 7px #777;*/
+ /*-webkit-box-shadow: 3px 3px 7px #777;*/
+ /*-moz-border-radius: 5px;*/
+ /*-webkit-border-radius: 5px;*/
+ /*z-index:999*/
+/*}*/
-.popupMessage input[type="button"]{
- width: 100px;
- margin: 5px;
-}
+/*.popupMessage h1{*/
+ /*text-align:center;*/
+ /*background:#6677AA;*/
+ /*border:1px solid #314763;*/
+ /*color:#FFFFFF !important;*/
+ /*font-size:11px;*/
+ /*font-weight:bold;*/
+ /*height:13px;*/
+ /*line-height:12px;*/
+ /*padding: 5px;*/
+/*}*/
+
+/*.popupMessage input[type="button"]{*/
+ /*width: 100px;*/
+ /*margin: 5px;*/
+/*}*/
/*div#selected_annotations label{*/
/*display: inline-block;*/
/*vertical-align: middle;*/
/*}*/
/*div#selected_annotations label input{*/
/*vertical-align: middle;*/
/*}*/
-/*POPUP 2*/
+/* POPUPS */
.hd {
color: #FFFFFF !important;
background: transparent !important;
background-image: url(images/top_hive.gif) !important;
background-repeat: repeat-x !important;
font-size:14px !important;
font-weight:bold !important;
cursor: move !important;
}
.bd {
background: #EFEFFF !important;
background:#FFF;
border:solid #63758C;
border-width:1px 0;
overflow:auto;
height:100%;
}
+.MedCo_popupTable{
+ border-spacing: 0px 15px;
+}
+
+.MedCo_popupTable th{
+ width: auto;
+}
+
.MedCo_popupTable tr td {
width: 400px;
}
.MedCo_popupTable tr td *{
width: 100%;
}
+#zygosityListGenePopup,
+#zygosityListVariantNamePopup{
+ margin: auto;
+ width: auto;
+ vertical-align: middle;
+ float: left;
+ border: 2px solid #d5d5d5;
+}
+
+#zygosityListGenePopup label,
+#zygosityListVariantNamePopup label{
+ margin-left: 10px;
+ margin-right: 7px;
+ width: auto;
+ float: left;
+}
+
+#zygosityListGenePopup input,
+#zygosityListVariantNamePopup input{
+ width: auto;
+ vertical-align: middle;
+}
/*reset and run Buttons*/
DIV#MedCo-TABS DIV.MED-Buttons {
padding-left:20px;
margin-bottom:10px;
overflow:hidden;
}
DIV#MedCo-TABS DIV.resetButton,
DIV#MedCo-TABS DIV.runButton {
position:relative;
xdisplay:none;
background:#6677AA;
border:1px solid #667788;
color:#FFFFFF;
font-weight:bold;
font-family:arial,helvetica;
font-size:11px;
height:16px;
line-height:16px;
text-align:center;
color:#FFF;
cursor:pointer;
float: left;
margin:0px 5px 0px 0px;
width:72px;
xz-index:5;
overflow:hidden;
}
DIV#MedCo-TABS DIV.resetButton a,
DIV#MedCo-TABS DIV.runButton a {
color:#FFF;
display:block;
text-decoration:none;
}
DIV#MedCo-TABS DIV.resetButton a:hover,
DIV#MedCo-TABS DIV.runButton a:hover {
background-color:#7687bf;
}
/*Result*/
DIV#MedCo-TABS table.MED-resultTable{
width: 400px;
margin-left: auto;
margin-right: auto;
}
/*"Number of patient"*/
DIV#MedCo-TABS table.MED-resultTable tr:first-child td{
background-color: #B0C4DE;
color: black;
text-align: center;
vertical-align: middle;
}
/*count*/
DIV#MedCo-TABS table.MED-resultTable tr:last-child td{
background-color: #B0C4DE;
color: darkblue;
text-align: center;
vertical-align: middle;
font-size: 45px;
}
/*loading query gif*/
img#MED-loadingGif {
width:47px;
height:47px;
display: none;
text-align: center;
vertical-align: middle;
margin-left: auto;
margin-right: auto;
}
diff --git a/js-i2b2/cells/plugins/MedCo/php/getAnnotationValues.php b/js-i2b2/cells/plugins/MedCo/php/getAnnotationValues.php
index a1146ab..d052db4 100644
--- a/js-i2b2/cells/plugins/MedCo/php/getAnnotationValues.php
+++ b/js-i2b2/cells/plugins/MedCo/php/getAnnotationValues.php
@@ -1,22 +1,22 @@
<?php
$conn = pg_connect("host=localhost port=5432 dbname=i2b2 user=postgres password=admin");
if (!$conn) {
echo "Error while connecting to the postgres database";
exit;
}
// get the row which contains all the values of the passed annotation
-$query = "SELECT annotation_values FROM shrine_ont.genomic_annotations_metadata WHERE annotation_id='". htmlspecialchars($_GET["annotation_name"]) . "'";
+$query = "SELECT annotation_values FROM shrine_ont.genomic_annotations_metadata WHERE annotation_id='". $_GET["annotation_name"] . "'";
$result = pg_query($conn, $query);
if (!$result) {
echo "An error occurred.\n";
exit;
}
// just tell to which annotation these values correspond (in case of concurrent requests there may be inconsistencies)
echo $_GET["annotation_name"] . "$%$";
while ($row = pg_fetch_row($result)) {
echo "$row[0]";
}
diff --git a/js-i2b2/cells/plugins/MedCo/php/getGenes.php b/js-i2b2/cells/plugins/MedCo/php/getGenes.php
index 35f4ee5..4f9f4cc 100644
--- a/js-i2b2/cells/plugins/MedCo/php/getGenes.php
+++ b/js-i2b2/cells/plugins/MedCo/php/getGenes.php
@@ -1,40 +1,40 @@
<?php
// case sensitive % stands for .*
//select *
//from shrine_ont.gene_values
//where gene_value LIKE '%A1%' //
//LIMIT 20
// case insensitive with regex
//select *
//from shrine_ont.gene_values
//where gene_value ~* '.*a1.*'
//LIMIT 20
$conn = pg_connect("host=localhost port=5432 dbname=i2b2 user=postgres password=admin");
if (!$conn) {
echo "Error while connecting to the postgres database";
exit;
}
// get the row which contains all the values of the passed annotation
$query =
"SELECT gene_value
FROM shrine_ont.gene_values
-WHERE gene_value ~* '.*" . htmlspecialchars($_GET["gene"]) .".*'
-LIMIT " . htmlspecialchars($_GET["limit"]);
+WHERE gene_value ~* '.*" . $_GET["gene"] .".*'
+LIMIT " . $_GET["limit"];
$result = pg_query($conn, $query);
if (!$result) {
echo "An error occurred.\n";
exit;
}
// In json format return the list of genes
$geneList = "";
while ($row = pg_fetch_row($result)) {
$geneList .= "\"$row[0]\",";
}
// drop the last comma and concatenate in json format
echo "[" . substr($geneList, 0, -1) . "]";
\ No newline at end of file
diff --git a/js-i2b2/cells/plugins/MedCo/php/getGenes.php b/js-i2b2/cells/plugins/MedCo/php/getVariantNames.php
similarity index 54%
copy from js-i2b2/cells/plugins/MedCo/php/getGenes.php
copy to js-i2b2/cells/plugins/MedCo/php/getVariantNames.php
index 35f4ee5..a8f9cd9 100644
--- a/js-i2b2/cells/plugins/MedCo/php/getGenes.php
+++ b/js-i2b2/cells/plugins/MedCo/php/getVariantNames.php
@@ -1,40 +1,36 @@
<?php
-// case sensitive % stands for .*
-//select *
-//from shrine_ont.gene_values
-//where gene_value LIKE '%A1%' //
-//LIMIT 20
-
// case insensitive with regex
-//select *
-//from shrine_ont.gene_values
-//where gene_value ~* '.*a1.*'
+//select variant_name
+//from shrine_ont.variant_names
+//where variant_name ~* '.*a1.*'
//LIMIT 20
$conn = pg_connect("host=localhost port=5432 dbname=i2b2 user=postgres password=admin");
if (!$conn) {
echo "Error while connecting to the postgres database";
exit;
}
+// escape the ? for regex query
+$variant_name = str_replace("?", "\?", $_GET["variant_name"]);
// get the row which contains all the values of the passed annotation
$query =
- "SELECT gene_value
-FROM shrine_ont.gene_values
-WHERE gene_value ~* '.*" . htmlspecialchars($_GET["gene"]) .".*'
-LIMIT " . htmlspecialchars($_GET["limit"]);
+ "SELECT variant_name
+FROM shrine_ont.variant_names
+WHERE variant_name ~* '.*" . $variant_name .".*'
+LIMIT " . $_GET["limit"];
$result = pg_query($conn, $query);
if (!$result) {
echo "An error occurred.\n";
exit;
}
// In json format return the list of genes
-$geneList = "";
+$variantNames = "";
while ($row = pg_fetch_row($result)) {
- $geneList .= "\"$row[0]\",";
+ $variantNames .= "\"$row[0]\",";
}
// drop the last comma and concatenate in json format
-echo "[" . substr($geneList, 0, -1) . "]";
\ No newline at end of file
+echo "[" . substr($variantNames, 0, -1) . "]";
\ No newline at end of file
diff --git a/js-i2b2/cells/plugins/MedCo/php/getVariants.php b/js-i2b2/cells/plugins/MedCo/php/getVariants.php
index 9e07bc6..caa4f69 100644
--- a/js-i2b2/cells/plugins/MedCo/php/getVariants.php
+++ b/js-i2b2/cells/plugins/MedCo/php/getVariants.php
@@ -1,56 +1,75 @@
<?php
// query_type define is we are searching by:
// - old is the old version that uses the first version of the schema
// - Gene + Zygosity
// - ...
+
$query = "";
-switch(htmlspecialchars($_GET["query_type"])){
+switch($_GET["query_type"]){
case "gene_and_zygosity":
+ // case insensitive regex query
// select variant_id
// from shrine_ont.genomic_annotations_new
- // where annotations ~* 'CTBP2P1;Homozygous;'
+ // where annotations ~* '^CTBP2P1;(Homozygous|Unknown);'
+
+ $zigosity = $_GET["zygosity"]; // array of zygosity options, put them in the query separated by | (or)
$query =
"SELECT variant_id " .
"FROM shrine_ont.genomic_annotations_new " .
- "WHERE annotations ~* '" . htmlspecialchars($_GET["gene_name"]) . ";" . htmlspecialchars($_GET["zygosyty"]) .";'";;
+ "WHERE annotations ~* '^" . $_GET["gene_name"] .
+ ";(" . join('|', $zigosity) .");'";
+ break;
+
+ case "variantName_and_zygosity":
+ // case insensitive regex query
+ // select variant_id
+ // from shrine_ont.genomic_annotations_new
+ /* where variant_name='Y:59022489:?>A'*/
+
+ $zigosity = $_GET["zygosity"];
+
+ $query = "SELECT variant_id " .
+ "FROM shrine_ont.genomic_annotations_new " .
+ "WHERE variant_name='" . $_GET["variant_name"] ."' AND " .
+ "annotations ~* '" . "(" . join('|', $zigosity) .")'";
break;
case "old":
//select variant_id
//from shrine_ont.genomic_annotations
//where variant_annotations ->> 'Start_Position' = '5239176'
$query =
"SELECT variant_id
FROM shrine_ont.genomic_annotations
-WHERE variant_annotations ->> '". htmlspecialchars($_GET["annotation_name"]) . "' = '" . htmlspecialchars($_GET["annotation_value"]) ."'";
+WHERE variant_annotations ->> '". $_GET["annotation_name"] . "' = '" . $_GET["annotation_value"] ."'";
break;
default:
echo "Error: query type not recognized";
return;
}
$conn = pg_connect("host=localhost port=5432 dbname=i2b2 user=postgres password=admin");
if (!$conn) {
echo "Error while connecting to the postgres database";
exit;
}
$result = pg_query($conn, $query);
if (!$result) {
echo "An error occurred.\n";
exit;
}
// In json format return both the panel number and the list of variants
echo "{ \"panel_number\" :" . $_GET["panel_number"] . ", \"variants\" : ";
$variantList = "";
while ($row = pg_fetch_row($result)) {
$variantList .= "\"$row[0]\",";
}
// drop the last comma
echo "[" . substr($variantList, 0, -1) . "]}";
\ No newline at end of file
diff --git a/js-i2b2/cells/plugins/MedCo/popup_ctrlr.js b/js-i2b2/cells/plugins/MedCo/popup_ctrlr.js
index 8763fa9..e36bcfa 100644
--- a/js-i2b2/cells/plugins/MedCo/popup_ctrlr.js
+++ b/js-i2b2/cells/plugins/MedCo/popup_ctrlr.js
@@ -1,654 +1,938 @@
i2b2.MedCo.popup = {};
// check the paths are correct
i2b2.MedCo.popup.getAnnotationPath = 'js-i2b2/cells/plugins/MedCo/getAnnotations.php';
// in getAnnotationValuesPath append a variable called 'annotation_name' to specify the annotation
i2b2.MedCo.popup.getAnnotationValuesPath = 'js-i2b2/cells/plugins/MedCo/getAnnotationValues.php';
// in getVariantsPath append two variables 'annotation_name' and 'annotation_value' to respectively specify
// the name and the value fo the annotation. Moreover, a variable 'panel_number' is needed too so to know
// to which panel correspond the received response.
i2b2.MedCo.popup.getVariantsPath = 'js-i2b2/cells/plugins/MedCo/getVariants.php';
// GENE POPUP
i2b2.MedCo.ctrlr.genePopup = {
dialog: null,
// variable to access easily the popup
popup: $("MedCo_genePopup"),
// input box in which the user will write. It is an <input type="search"> element
geneInputBox: document.querySelector("#searchGeneInputBox"),
// selection list to display the matching genes. It is a <select> element
geneList: document.querySelector("#geneList"),
// selection list with the 4 predefined options
- zygosityList: document.querySelector("#zygosityList"),
+ zygosityList: {
+ heterozygousCheckbox:null,
+ homozygousCheckbox:null,
+ unknownCheckbox:null
+ },
// variable used for the popup to know to which panel it is bound
panelNumber: 0, // todo set this when opening the popup (at the drag)
// initialize the gene popup
init: function(){
var context = i2b2.MedCo.ctrlr.genePopup;
context.popup = $("MedCo_genePopup");
context.geneInputBox = document.querySelector("#searchGeneInputBox");
context.geneList = document.querySelector("#geneList");
- context.zygosityList = document.querySelector("#zygosityList");
+
+ // the three checkboxes
+ context.zygosityList.heterozygousCheckbox = document.querySelector("#heterozygousGenePopup");
+ context.zygosityList.homozygousCheckbox = document.querySelector("#homozygousGenePopup");
+ context.zygosityList.unknownCheckbox = document.querySelector("#unknownGenePopup");
// update the scrolldown list every time the user digits chars
context.geneInputBox
.addEventListener("keyup", context.getGenes.run);
context.panelNumber = 0;
context.getGenes.path = 'js-i2b2/cells/plugins/MedCo/php/getGenes.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.genePopup;
// validate the fields
if (context.geneList.options.length < 1){
// todo: can the user not put any gene name and just search by zygosity? (most probably too many variants)
// if the drop down list is empty then
- alert("Please, write down a gene name and pick one form the dropdown list.");
+ alert("Please, write down a gene name and pick one choice form the dropdown list.");
+ return;
+ }
+ if (context.zygosityList.heterozygousCheckbox.checked == false &&
+ context.zygosityList.homozygousCheckbox.checked == false &&
+ context.zygosityList.unknownCheckbox.checked == false) {
+ alert("Please, select at least one zygosity option.");
return;
}
if (context.geneInputBox.value.toLowerCase() != context.geneList.options[context.geneList.selectedIndex].text.toLowerCase()){
// if it is different then the user has still to pick one from the dropdown list
alert("Please, pick a gene name from the dropdown list.");
return;
}
// run the query to retrieve all the annotations with the specified gene and zygosyty
i2b2.MedCo.ctrlr.genePopup.getVariants.run();
this.hide()
};
context.dialog = new YAHOO.widget.SimpleDialog("MedCo_genePopup", {
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.genePopup;
context.panelNumber = panelNumber;
// context.clear();
context.popup.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.genePopup.popup.hide();
// i2b2.MedCo.ctrlr.genePopup.dialog.cancel();
// },
// clear (empty) all the elements
clear: function(){
// i2b2.MedCo.ctrlr.genePopup.geneInputBox.value = "";
// var list = i2b2.MedCo.ctrlr.genePopup.geneList;
// while (list.hasChildNodes()) {
// list.removeChild(list.lastChild);
// }
// todo clear fields?
},
// get the genes names from the database
getGenes: {
// Store some variables I need to efficiently manage the request
// path for the php request to retrieve the genes
path: 'js-i2b2/cells/plugins/MedCo/getGenes.php',
// if previousGene (which stores the "old" geneInputBox content) stays the same for a certain period
// of time then the user stopped writing => I retrieve from the database the matching genes
previousGene: "",
// here I store the last executed query so to avoid repeating it
lastGeneQueried: "",
// here I store the current timeout (so that I can stop it when I want)
timeoutGene: null,
run: function () {
var context = i2b2.MedCo.ctrlr.genePopup.getGenes;
// (call run until the user stops writing)
// stop the previous call (every new digits trigger a getGenes() call)
clearTimeout(context.timeoutGene);
// take the current value and check if it is equal to the previous one
var currGene = i2b2.MedCo.ctrlr.genePopup.geneInputBox.value.replace(/\s/g, ''); // remove whitespaces
if (currGene == ""){
// if it is empty then just empty the dropdown list
var list = i2b2.MedCo.ctrlr.genePopup.geneList;
while (list.hasChildNodes()) {
list.removeChild(list.lastChild);
}
+ context.lastGeneQueried = "";
return;
}
if (currGene == context.lastGeneQueried) {
- // if it is equal to the previous query then do nothing
- context.lastGeneQueried = "";
+ // if it is equal to the previous queried then I already have all the matching ones => do nothing
return;
}
if (currGene != context.previousGene) {
// if they were different then wait for the user to finish to write
context.previousGene = currGene;
context.timeoutGene = setTimeout(context.run, 500);
return;
}
// If you ended up here then the user stopped writing and we can execute the query
context.lastGeneQueried = currGene; // store the current query so to avoid repeating it
var success = function (responseText) {
var list = i2b2.MedCo.ctrlr.genePopup.geneList;
// remove all the previous genes from the dropdown list
while (list.hasChildNodes()) {
list.removeChild(list.lastChild);
}
// todo sort the genes
var receivedGenes = JSON.parse(responseText);
for (var i = 0; i < receivedGenes.length; i++) {
var opt = document.createElement("option");
opt.value = receivedGenes[i];
opt.innerHTML = receivedGenes[i];
list.appendChild(opt);
}
// if there was only one match the copy that in the text box
if (receivedGenes.length == 1) {
i2b2.MedCo.ctrlr.genePopup.geneInputBox.value = receivedGenes[0];
}
};
var error = function (err) {
alert("Error when trying to retrieve the gene values from the database: " + err)
};
var phpQuery =
context.path +
"?gene=" + currGene +
"&limit=20"; // todo is it ok 20?
i2b2.MedCo.ctrlr.phpGETRequest(success, error, phpQuery);
}
},
// run the query to retrieve the id of the variants
getVariants: {
path: 'js-i2b2/cells/plugins/MedCo/getVariants.php',
run: function () {
var context = i2b2.MedCo.ctrlr.genePopup;
var geneName = context.geneInputBox.value;
- var zygosyty = context.zygosityList.options[context.zygosityList.selectedIndex].text;
+ 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")
+ }
+
var queryType = "gene_and_zygosity"; // used at the server side to know how to build the query
var success = function (responseText) {
+ alert(responseText)
var response = JSON.parse(responseText);
for(var i=0; i<response.variants.length; i++)
{
i2b2.MedCo.model.panels[response.panel_number].push(response.variants[i]);
}
// I received the response so decrease the counter
i2b2.MedCo.popup.variantsQueryCounter -= 1;
};
var error = function (err) {
- alert("Error when trying to retrieve the gene values from the database: " + 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.variantsQueryCounter += 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.getVariants.path +
"?query_type=" + queryType +
"&panel_number=" + context.panelNumber +
"&gene_name=" + geneName +
- "&zygosyty=" + zygosyty;
+ "&zygosity[]=" + zygosyty.join("&zygosity[]="); // build an array of zygosity options
i2b2.MedCo.ctrlr.phpGETRequest(success, error, phpQuery);
}
}
};
-// 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
-i2b2.MedCo.ctrlr.phpGETRequest = function (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;
+// VARIANT NAME POPUP
+i2b2.MedCo.ctrlr.variantNamePopup = {
+ dialog: null,
+ // variable to access easily the popup
+ popup: $("MedCo_variantNamePopup"),
- // 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);
- }
- };
+ // input box in which the user will write. It is an <input type="search"> element
+ variantNameInputBox: document.querySelector("#searchVariantNameInputBox"),
- req.open("GET", phpQuery, true);
- req.send(null);
- return req;
-};
+ // selection list to display the matching VARIANT NAMES. It is a <select> element
+ variantNameList: document.querySelector("#variantNameList"),
+ // selection list with the 4 predefined options
+ zygosityList: {
+ heterozygousCheckbox:null,
+ homozygousCheckbox:null,
+ unknownCheckbox:null
+ },
-// initialize the popup: load the names of the annotations and register handlers to manage the automatic completion
-i2b2.MedCo.ctrlr.PopupInit = function (){
- // get the element to register the event handler (auto completion)
- var searchAnnotationBox = document.querySelector("#searchAnnotationBox");
- var annotations = document.querySelector("#annotationList"); // this will be loaded with all the annotations
-
- var searchAnnotationValueBox = document.querySelector("#searchAnnotationValueBox");
- var selectedAnnotationValue = document.querySelector("#selectedAnnotationValue");
- // (inefficient) var annotationValues = document.querySelector("#annotationValueList"); // this will be loaded with all the values an annotation can assume
-
- // load annotations from database (that will be shown when opening the popup)
- // the annotations name are loaded immediately (they are not too many) while the values of an annotation
- // are loaded only when that annotation is selected
- i2b2.MedCo.ctrlr.loadAnnotations();
-
- // autocompletion function, e is an <input type="search"> object, list is a <select> object
- function autoCompletionAnnotation (e, list) {
- var text = e.target.value;
- var lowerText = text.toLowerCase();
- var options = list.options;
- var initialOption = options[list.selectedIndex].text;
- var goodMatch = false;
- for (var i = 0; i < options.length; i++) {
- var option = options[i];
- var optionText = option.text;
- var regex = new RegExp("^" + text, "i");
- var match = optionText.match(regex);
- // best match
- if (match){ // if it starts the same the select this one
- option.selected = true;
- break;
- }
- // good match (still looking for a best match)
- var contains = optionText.indexOf(text) != -1;
- if(contains) {
- option.selected = true;
- goodMatch = true;
- }
- if (!goodMatch) { // if no good match was found then try this too
- // worse match (still looking for a good or best match)
- var lowerOptionText = optionText.toLowerCase();
- contains = lowerOptionText.indexOf(lowerText) != -1;
- if (contains) { // it contains the string select this one but go on with looking for a better match
- option.selected = true;
- }
- }
- option.selectedIndex = 0;
- }
- // if the selected annotation changed then reload its values
- var currOption = options[list.selectedIndex].text;
- if (initialOption != currOption) {
- // want to reduce the number of "loadAnnotationValues", if after some time the option didn't changed
- // then I suppose the user stopped typing
- setTimeout(
- function(){
- if(currOption == list.options[list.selectedIndex].text)
- i2b2.MedCo.ctrlr.loadAnnotationValues()
- }, 500);
- }
- }
+ // variable used for the popup to know to which panel it is bound
+ panelNumber: 0, // todo set this when opening the popup (at the drag)
- // showValue is an html object in which we will show the value
- function autoCompletionAnnotationValue (e, showValue) {
- var text = e.target.value;
- var lowerText = text.toLowerCase();
- var values = i2b2.MedCo.popup.annotationValues; // list of possible values []string
- var goodMatch = false;
- for (var i = 0; i < values.length; i++) {
- var valueText = values[i];
- var regex = new RegExp("^" + text, "i");
- var match = valueText.match(regex);
- // best match
- if (match){ // if it starts the same the select this one
- showValue.innerHTML = valueText;
- break;
- }
- // good match (still looking for a best match)
- var contains = valueText.indexOf(text) != -1;
- if(contains) {
- showValue.innerHTML = valueText;
- goodMatch = true;
- }
- if (!goodMatch) { // if no good match was found then try this too
- // worse match (still looking for a good or best match)
- var lowerValueText = valueText.toLowerCase();
- contains = lowerValueText.indexOf(lowerText) != -1;
- if (contains) { // it contains the string select this one but go on with looking for a better match
- showValue.innerHTML = valueText;
+ // initialize the variant popup
+ init: function(){
+ var context = i2b2.MedCo.ctrlr.variantNamePopup;
- }
- }
- }
- }
+ context.popup = $("MedCo_variantNamePopup");
+ context.variantNameInputBox = document.querySelector("#searchVariantNameInputBox");
+ context.variantNameList = document.querySelector("#variantNameList");
- // autocomplete the annotation name when entered
- searchAnnotationBox.addEventListener("keyup", function (e) {autoCompletionAnnotation(e, annotations)});
+ // the three checkboxes
+ context.zygosityList.heterozygousCheckbox = document.querySelector("#heterozygousVariantNamePopup");
+ context.zygosityList.homozygousCheckbox = document.querySelector("#homozygousVariantNamePopup");
+ context.zygosityList.unknownCheckbox = document.querySelector("#unknownVariantNamePopup");
- // autocomplete the annotation value when entered
- searchAnnotationValueBox.addEventListener("keyup", function (e) {autoCompletionAnnotationValue(e, selectedAnnotationValue)});
+ // update the scrolldown list every time the user digits chars
+ context.variantNameInputBox
+ .addEventListener("keyup",
+ context.getVariantNames.run
+ );
+ context.panelNumber = 0;
- // variable used for the popup to know to which panel it is bound
- i2b2.MedCo.popup.panelNumber = 0;
- //variable to know which is the latest pending request sent for annotation values retrieval (the previous ones will be dropped)
- i2b2.MedCo.popup.latestAnnotationRequest = "";
+ context.getVariantNames.path = 'js-i2b2/cells/plugins/MedCo/php/getVariantNames.php';
+ context.getVariants.path = 'js-i2b2/cells/plugins/MedCo/php/getVariants.php';
- // store the current loaded annotation values
- i2b2.MedCo.popup.annotationValues = [];
+ var handleCancel = function() {
+ this.cancel();
+ };
- // a counter used to count how many queries the client sent and is still waiting for a response.
- // while this counter is > 0 the query cannot be built
- i2b2.MedCo.popup.variantsQueryCounter = 0;
-};
+ var handleOk = function() {
+ var context = i2b2.MedCo.ctrlr.variantNamePopup;
-i2b2.MedCo.popupShow = function (panelNumber) {
- i2b2.MedCo.popup.panelNumber = panelNumber;
- var messageBox=document.getElementById("annoMessage");
- // Center the messageBox
- // alert(messageBox.style.clientWidth)
- // messageBox.style.marginTop=-messageBox.style.height/2;
- // messageBox.style.marginLeft=-messageBox.style.width/2;
-
- // Show message box (and background)
- document.getElementById("MedCo_popupBackground").style.display="block";
- messageBox.style.display="block";
-};
+ // validate the fields
+ if (context.variantNameList.options.length < 1){
+ // if the drop down list is empty then
+ alert("Please, write down a variant name and pick one choice form the dropdown list.");
+ return;
+ }
+ if (context.zygosityList.heterozygousCheckbox.checked == false &&
+ context.zygosityList.homozygousCheckbox.checked == false &&
+ context.zygosityList.unknownCheckbox.checked == false) {
+ alert("Please, select at least one zygosity option.");
+ return;
+ }
+ if (context.variantNameInputBox.value.toLowerCase() !=
+ context.variantNameList.options[context.variantNameList.selectedIndex].text.toLowerCase()){
+ // if it is different then the user has still to pick one from the dropdown list
+ alert("Please, pick a variant name from the dropdown list.");
+ return;
-i2b2.MedCo.popupHide = function (){
- document.getElementById("MedCo_popupBackground").style.display="none";
- document.getElementById("annoMessage").style.display="none";
-};
+ }
-// i2b2.MedCo.popupEnterPressed = function (e) {
-// e = e || window.event;
-// if (e.keyCode == 13) // if enter is pressed ...
-// {
-// i2b2.MedCo.popupOk()
-// }
-// };
+ // run the query to retrieve all the annotations with the specified variant name and zygosyty
+ i2b2.MedCo.ctrlr.variantNamePopup.getVariants.run();
+ this.hide()
+ };
-i2b2.MedCo.popupOk = function(){
- // chosenAnnotationsElem = document.getElementById("chosen_annotations");
- // chosenAnnotationsElem.innerHTML = "";
+ context.dialog = new YAHOO.widget.SimpleDialog("MedCo_variantNamePopup", {
+ 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
+ }]
+ });
+ },
- // var annotations = document.querySelector("#annotationList");
- // var selectedAnnotation = annotations.options[annotations.selectedIndex].text;
- //
- // var selectedAnnotationValue = document.querySelector("#selectedAnnotationValue").innerHTML;
- // var annotationValues = document.querySelector("#annotationValueList");
- // var selectedAnnotationValue = annotationValues.options[annotationValues.selectedIndex].text;
+ // show the popup
+ // panelNumber: specifies with which panel is the popup related
+ show: function(panelNumber) {
+ var context = i2b2.MedCo.ctrlr.variantNamePopup;
+ context.panelNumber = panelNumber;
+ // context.clear();
+ context.popup.show();
+ context.dialog.render(document.body);
+ context.dialog.show();
+ },
- // var annoVal = selectedAnnotation+":"+selectedAnnotationValue;
+ // // hide the popup, not needed (events already registered to the various buttons)
+ // hide: function(){
+ // i2b2.MedCo.ctrlr.variantNamePopup.popup.hide();
+ // i2b2.MedCo.ctrlr.variantNamePopup.dialog.cancel();
+ // },
- // i2b2.MedCo.model.chosenAnnotations[i2b2.MedCo.popup.panelNumber].push(annoVal);
+ // clear (empty) all the elements
+ clear: function(){
+ // i2b2.MedCo.ctrlr.variantNamePopup.variantNameInputBox.value = "";
+ // var list = i2b2.MedCo.ctrlr.variantNamePopup.variantNameList;
+ // while (list.hasChildNodes()) {
+ // list.removeChild(list.lastChild);
+ // }
+ // todo clear fields?
+ },
- // i2b2.MedCo.view.panels[i2b2.MedCo.popup.panelNumber].innerHTML += annoVal + "<br>";
+ // get the variant names from the database
+ getVariantNames: {
+ // Store some variables I need to efficiently manage the request
+ // path for the php request to retrieve the variant names
+ path: 'js-i2b2/cells/plugins/MedCo/php/getVariantNames.php',
+ // if previousVariant (which stores the "old" variantNameInputBox content) stays the same for a certain period
+ // of time then the user stopped writing => I retrieve from the database the matching variant names
+ previousVariantName: "",
+ // here I store the last executed query so to avoid repeating it
+ lastVariantQueried: "",
+ // here I store the current timeout (so that I can stop it when I want)
+ timeoutVariant: null,
+ run: function () {
+ var context = i2b2.MedCo.ctrlr.variantNamePopup.getVariantNames;
- i2b2.MedCo.ctrlr.loadVariants(); // send php request
- i2b2.MedCo.popupHide();
-};
+ // (call run until the user stops writing)
+ // stop the previous call (every new digits trigger a getVariantNames() call)
+ clearTimeout(context.timeoutVariant);
+ // take the current value and check if it is equal to the previous one
+ var currVariantName = i2b2.MedCo.ctrlr.variantNamePopup.variantNameInputBox.value.replace(/\s/g, ''); // remove whitespaces
+ if (currVariantName == ""){
+ // if it is empty then just empty the dropdown list
+ var list = i2b2.MedCo.ctrlr.variantNamePopup.variantNameList;
+ while (list.hasChildNodes()) {
+ list.removeChild(list.lastChild);
+ }
+ context.lastVariantQueried = "";
+ return;
+ }
+ if (currVariantName == context.lastVariantQueried) {
+ // if it is equal to the previous query then do nothing
+ return;
+ }
+ if (currVariantName != context.previousVariantName) {
+ // if they are different then wait for the user to finish to write
+ context.previousVariantName = currVariantName;
+ context.timeoutVariant = setTimeout(context.run, 500);
+ return;
+ }
-// MANAGE PHP REQUEST
+ // If you ended up here then the user stopped writing and we can execute the query
+ context.lastVariantQueried = currVariantName; // store the current query so to avoid repeating it
-// load the annotations from the database (done only when initializing the popup!)
-i2b2.MedCo.ctrlr.loadAnnotations = function () {
- // 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;
+ var success = function (responseText) {
+ var list = i2b2.MedCo.ctrlr.variantNamePopup.variantNameList;
+ // remove all the previous variant names from the dropdown list
+ while (list.hasChildNodes()) {
+ list.removeChild(list.lastChild);
+ }
+ // todo sort the variant names
+ var receivedVariantNames= JSON.parse(responseText);
+ for (var i = 0; i < receivedVariantNames.length; i++) {
+ var opt = document.createElement("option");
+ opt.value = receivedVariantNames[i];
+ opt.innerHTML = receivedVariantNames[i];
+ list.appendChild(opt);
+ }
- // define two functions to manage the result received by the server
- var success = function (responseText) {
- // load the popup with the annotation names (you receive a json list of strings)
- var annotations = document.querySelector("#annotationList");
+ // if there was only one match the copy that in the text box
+ if (receivedVariantNames.length == 1) {
+ i2b2.MedCo.ctrlr.variantNamePopup.variantNameInputBox.value = receivedVariantNames[0];
+ }
+ };
+ var error = function (err) {
+ alert("Error when trying to retrieve the variant names from the database: " + err)
+ };
- // remove all children
- while (annotations.hasChildNodes()) {
- annotations.removeChild(annotations.lastChild);
- }
- // todo sort the annotations
- var receivedAnnotations = JSON.parse(responseText);
- for(var i=0; i<receivedAnnotations.length; i++)
- {
- var opt = document.createElement("option");
- opt.value = receivedAnnotations[i];
- opt.innerHTML = receivedAnnotations[i];
- annotations.appendChild(opt);
+ var phpQuery =
+ context.path +
+ "?variant_name=" + currVariantName +
+ "&limit=20"; // todo is it ok 20?
+ i2b2.MedCo.ctrlr.phpGETRequest(success, error, phpQuery);
}
- i2b2.MedCo.ctrlr.loadAnnotationValues();
- };
- var error = function (err) {
- alert("Error when trying to retrieve the annotations from the database." + err)
- };
+ },
- // 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);
- }
- };
+ // run the query to retrieve the id of the variants
+ getVariants: {
+ path: 'js-i2b2/cells/plugins/MedCo/php/getVariants.php',
- req.open("GET", i2b2.MedCo.popup.getAnnotationPath, true);
- req.send(null);
- return req;
-};
+ run: function () {
+ var context = i2b2.MedCo.ctrlr.variantNamePopup;
-i2b2.MedCo.ctrlr.loadAnnotationValues = function (){
- // just reset the two elements relative to the annotation value
- var selectedAnnotationValue = document.querySelector("#selectedAnnotationValue");
- selectedAnnotationValue.innerHTML = "";
- var searchAnnotationValueBox = document.querySelector("#searchAnnotationValueBox");
- searchAnnotationValueBox.innerHTML = "";
-
- // don't use the select anymore
- // var annotationValues = document.querySelector("#annotationValueList");
- // // remove all options
- // while (annotationValues.firstChild) {
- // annotationValues.removeChild(annotationValues.firstChild);
- // }
-
- // show that we are loading the values
- // document.getElementById("MED-loadingValues").innerHTML = "<img id=\"MED-LoadingValuesGif\" width=\"15px\" src=\"assets/images/spin.gif\">";
- // document.getElementById("MED-LoadingValuesGif").style.display = 'block';
-
- // 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;
+ var variantName = context.variantNameInputBox.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")
}
- }
- }
- // if the http request obj has not been created then return
- if (!req) return false;
-
- // define two functions to manage the result received by the server
- var success = function (responseText) {
- // $%$ is used as delimeter (AnnotationName$%$[val1,...,valn])
- var response = responseText.split("$%$");
- if (response[0] != i2b2.MedCo.popup.latestAnnotationRequest){
- // if I received an old response just ignore it
- return
- }
- var receivedValues = JSON.parse(response[1].slice(1, -1));
- // load the annotation values in the popup
- // var annotationValues = document.querySelector("#annotationValueList"); // don't use anymore the select
- i2b2.MedCo.popup.annotationValues = [];
- for(var i = 0; i < receivedValues.length; i++)
- {
- i2b2.MedCo.popup.annotationValues.push(receivedValues[i].toString());
- // var opt = document.createElement("option");
- // opt.value = receivedValues[i];
- // opt.innerHTML = receivedValues[i];
- // annotationValues.appendChild(opt);
- }
- // hide the loading gif
- // document.getElementById("MED-LoadingValuesGif").style.display = 'none';
- };
- var error = function (err) {
- alert("Error when trying to retrieve the values of the annotation from the database."+err)
- };
+ var queryType = "variantName_and_zygosity"; // used at the server side to know how to build the query
- // 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);
- }
- };
+ var success = function (responseText) {
+ alert(responseText); // todo delete
+ var response = JSON.parse(responseText);
+ for(var i=0; i<response.variants.length; i++)
+ {
+ i2b2.MedCo.model.panels[response.panel_number].push(response.variants[i]);
+ }
+ // I received the response so decrease the counter
+ i2b2.MedCo.popup.variantsQueryCounter -= 1;
+ };
+ var error = function (err) {
+ alert("Error when trying to retrieve the variants from the database: " + err)
+ };
- // get the selected annotation
- var annotations = document.querySelector("#annotationList");
- var selectedAnnotation = annotations.options[annotations.selectedIndex].value;
- // store it so that I will know if the answer is the most recent
- i2b2.MedCo.popup.latestAnnotationRequest = selectedAnnotation;
+ // increase the number of responses I should wait for
+ i2b2.MedCo.ctrlr.variantsQueryCounter += 1;
- req.open("GET", i2b2.MedCo.popup.getAnnotationValuesPath + "?annotation_name=" + selectedAnnotation , true);
- req.send(null);
- return req;
+ // 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.getVariants.path +
+ "?query_type=" + queryType +
+ "&panel_number=" + context.panelNumber +
+ "&variant_name=" + variantName +
+ "&zygosity[]=" + zygosyty.join("&zygosity[]="); // build an array of zygosity options
+ i2b2.MedCo.ctrlr.phpGETRequest(success, error, phpQuery);
+ }
+ }
};
-i2b2.MedCo.ctrlr.loadVariants = function (){
+// 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
+i2b2.MedCo.ctrlr.phpGETRequest = function (success, error, phpQuery) {
// create the request object to send the request and manage the response
var req = false;
- try{
+ try {
// most browsers
req = new XMLHttpRequest();
- } catch (e){
+ } catch (e) {
// IE
- try{
+ try {
req = new ActiveXObject("Msxml2.XMLHTTP");
- } catch(e) {
+ } catch (e) {
// try an older version
- try{
+ try {
req = new ActiveXObject("Microsoft.XMLHTTP");
- } catch(e) {
+ } catch (e) {
return false;
}
}
}
// if the http request obj has not been created then return
if (!req) return false;
- // define two functions to manage the result received by the server
- var success = function (responseText) {
- var response = JSON.parse(responseText);
- for(var i=0; i<response.variants.length; i++)
- {
- i2b2.MedCo.model.panels[response.panel_number].push(response.variants[i]);
- }
- // I received the response so decrease the counter
- i2b2.MedCo.popup.variantsQueryCounter -= 1;
- };
- var error = function (err) {
- alert("Error when trying to retrieve the variants from the database."+err)
- };
// update the request object to act when receiving the response
- req.onreadystatechange = function(){
- if(req.readyState == 4) {
+ req.onreadystatechange = function () {
+ if (req.readyState == 4) {
return req.status === 200 ?
success(req.responseText) : error(req.status);
}
};
- // just write down that there is one more response we are waiting for
- i2b2.MedCo.popup.variantsQueryCounter += 1;
+ req.open("GET", phpQuery, true);
+ req.send(null);
+ return req;
+};
- var annotations = document.querySelector("#annotationList");
- var selectedAnnotation = annotations.options[annotations.selectedIndex].value;
- var selectedValue = document.querySelector("#selectedAnnotationValue").innerHTML;
- req.open("GET", i2b2.MedCo.popup.getVariantsPath +
- "?annotation_name=" + selectedAnnotation +
- "&annotation_value=" + selectedValue +
- "&panel_number=" + i2b2.MedCo.popup.panelNumber, true);
- req.send(null);
- return req;
-};
\ No newline at end of file
+// OLD POPUP, TODO DELETE
+// // initialize the popup: load the names of the annotations and register handlers to manage the automatic completion
+// i2b2.MedCo.ctrlr.PopupInit = function (){
+// // get the element to register the event handler (auto completion)
+// var searchAnnotationBox = document.querySelector("#searchAnnotationBox");
+// var annotations = document.querySelector("#annotationList"); // this will be loaded with all the annotations
+//
+// var searchAnnotationValueBox = document.querySelector("#searchAnnotationValueBox");
+// var selectedAnnotationValue = document.querySelector("#selectedAnnotationValue");
+// // (inefficient) var annotationValues = document.querySelector("#annotationValueList"); // this will be loaded with all the values an annotation can assume
+//
+// // load annotations from database (that will be shown when opening the popup)
+// // the annotations name are loaded immediately (they are not too many) while the values of an annotation
+// // are loaded only when that annotation is selected
+// i2b2.MedCo.ctrlr.loadAnnotations();
+//
+// // autocompletion function, e is an <input type="search"> object, list is a <select> object
+// function autoCompletionAnnotation (e, list) {
+// var text = e.target.value;
+// var lowerText = text.toLowerCase();
+// var options = list.options;
+// var initialOption = options[list.selectedIndex].text;
+// var goodMatch = false;
+// for (var i = 0; i < options.length; i++) {
+// var option = options[i];
+// var optionText = option.text;
+// var regex = new RegExp("^" + text, "i");
+// var match = optionText.match(regex);
+// // best match
+// if (match){ // if it starts the same the select this one
+// option.selected = true;
+// break;
+// }
+// // good match (still looking for a best match)
+// var contains = optionText.indexOf(text) != -1;
+// if(contains) {
+// option.selected = true;
+// goodMatch = true;
+// }
+// if (!goodMatch) { // if no good match was found then try this too
+// // worse match (still looking for a good or best match)
+// var lowerOptionText = optionText.toLowerCase();
+// contains = lowerOptionText.indexOf(lowerText) != -1;
+// if (contains) { // it contains the string select this one but go on with looking for a better match
+// option.selected = true;
+// }
+// }
+// option.selectedIndex = 0;
+// }
+// // if the selected annotation changed then reload its values
+// var currOption = options[list.selectedIndex].text;
+// if (initialOption != currOption) {
+// // want to reduce the number of "loadAnnotationValues", if after some time the option didn't changed
+// // then I suppose the user stopped typing
+// setTimeout(
+// function(){
+// if(currOption == list.options[list.selectedIndex].text)
+// i2b2.MedCo.ctrlr.loadAnnotationValues()
+// }, 500);
+// }
+// }
+//
+// // showValue is an html object in which we will show the value
+// function autoCompletionAnnotationValue (e, showValue) {
+// var text = e.target.value;
+// var lowerText = text.toLowerCase();
+// var values = i2b2.MedCo.popup.annotationValues; // list of possible values []string
+// var goodMatch = false;
+// for (var i = 0; i < values.length; i++) {
+// var valueText = values[i];
+// var regex = new RegExp("^" + text, "i");
+// var match = valueText.match(regex);
+// // best match
+// if (match){ // if it starts the same the select this one
+// showValue.innerHTML = valueText;
+// break;
+// }
+// // good match (still looking for a best match)
+// var contains = valueText.indexOf(text) != -1;
+// if(contains) {
+// showValue.innerHTML = valueText;
+// goodMatch = true;
+// }
+// if (!goodMatch) { // if no good match was found then try this too
+// // worse match (still looking for a good or best match)
+// var lowerValueText = valueText.toLowerCase();
+// contains = lowerValueText.indexOf(lowerText) != -1;
+// if (contains) { // it contains the string select this one but go on with looking for a better match
+// showValue.innerHTML = valueText;
+//
+// }
+// }
+// }
+// }
+//
+// // autocomplete the annotation name when entered
+// searchAnnotationBox.addEventListener("keyup", function (e) {autoCompletionAnnotation(e, annotations)});
+//
+// // autocomplete the annotation value when entered
+// searchAnnotationValueBox.addEventListener("keyup", function (e) {autoCompletionAnnotationValue(e, selectedAnnotationValue)});
+//
+//
+// // variable used for the popup to know to which panel it is bound
+// i2b2.MedCo.popup.panelNumber = 0;
+// //variable to know which is the latest pending request sent for annotation values retrieval (the previous ones will be dropped)
+// i2b2.MedCo.popup.latestAnnotationRequest = "";
+//
+// // store the current loaded annotation values
+// i2b2.MedCo.popup.annotationValues = [];
+//
+// // a counter used to count how many queries the client sent and is still waiting for a response.
+// // while this counter is > 0 the query cannot be built
+// i2b2.MedCo.popup.variantsQueryCounter = 0;
+// };
+//
+// i2b2.MedCo.popupShow = function (panelNumber) {
+// i2b2.MedCo.popup.panelNumber = panelNumber;
+// var messageBox=document.getElementById("annoMessage");
+// // Center the messageBox
+// // alert(messageBox.style.clientWidth)
+// // messageBox.style.marginTop=-messageBox.style.height/2;
+// // messageBox.style.marginLeft=-messageBox.style.width/2;
+//
+// // Show message box (and background)
+// document.getElementById("MedCo_popupBackground").style.display="block";
+// messageBox.style.display="block";
+// };
+//
+// i2b2.MedCo.popupHide = function (){
+// document.getElementById("MedCo_popupBackground").style.display="none";
+// document.getElementById("annoMessage").style.display="none";
+// };
+//
+// // i2b2.MedCo.popupEnterPressed = function (e) {
+// // e = e || window.event;
+// // if (e.keyCode == 13) // if enter is pressed ...
+// // {
+// // i2b2.MedCo.popupOk()
+// // }
+// // };
+//
+// i2b2.MedCo.popupOk = function(){
+// // chosenAnnotationsElem = document.getElementById("chosen_annotations");
+// // chosenAnnotationsElem.innerHTML = "";
+//
+// // var annotations = document.querySelector("#annotationList");
+// // var selectedAnnotation = annotations.options[annotations.selectedIndex].text;
+// //
+// // var selectedAnnotationValue = document.querySelector("#selectedAnnotationValue").innerHTML;
+// // var annotationValues = document.querySelector("#annotationValueList");
+// // var selectedAnnotationValue = annotationValues.options[annotationValues.selectedIndex].text;
+//
+//
+// // var annoVal = selectedAnnotation+":"+selectedAnnotationValue;
+//
+// // i2b2.MedCo.model.chosenAnnotations[i2b2.MedCo.popup.panelNumber].push(annoVal);
+//
+// // i2b2.MedCo.view.panels[i2b2.MedCo.popup.panelNumber].innerHTML += annoVal + "<br>";
+//
+//
+// i2b2.MedCo.ctrlr.loadVariants(); // send php request
+// i2b2.MedCo.popupHide();
+// };
+//
+// // MANAGE PHP REQUEST
+//
+// // load the annotations from the database (done only when initializing the popup!)
+// i2b2.MedCo.ctrlr.loadAnnotations = function () {
+// // 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;
+//
+// // define two functions to manage the result received by the server
+// var success = function (responseText) {
+// // load the popup with the annotation names (you receive a json list of strings)
+// var annotations = document.querySelector("#annotationList");
+//
+// // remove all children
+// while (annotations.hasChildNodes()) {
+// annotations.removeChild(annotations.lastChild);
+// }
+// // todo sort the annotations
+// var receivedAnnotations = JSON.parse(responseText);
+// for(var i=0; i<receivedAnnotations.length; i++)
+// {
+// var opt = document.createElement("option");
+// opt.value = receivedAnnotations[i];
+// opt.innerHTML = receivedAnnotations[i];
+// annotations.appendChild(opt);
+// }
+// i2b2.MedCo.ctrlr.loadAnnotationValues();
+// };
+// var error = function (err) {
+// alert("Error when trying to retrieve the annotations from the database." + err)
+// };
+//
+// // 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", i2b2.MedCo.popup.getAnnotationPath, true);
+// req.send(null);
+// return req;
+// };
+//
+// i2b2.MedCo.ctrlr.loadAnnotationValues = function (){
+// // just reset the two elements relative to the annotation value
+// var selectedAnnotationValue = document.querySelector("#selectedAnnotationValue");
+// selectedAnnotationValue.innerHTML = "";
+// var searchAnnotationValueBox = document.querySelector("#searchAnnotationValueBox");
+// searchAnnotationValueBox.innerHTML = "";
+//
+// // don't use the select anymore
+// // var annotationValues = document.querySelector("#annotationValueList");
+// // // remove all options
+// // while (annotationValues.firstChild) {
+// // annotationValues.removeChild(annotationValues.firstChild);
+// // }
+//
+// // show that we are loading the values
+// // document.getElementById("MED-loadingValues").innerHTML = "<img id=\"MED-LoadingValuesGif\" width=\"15px\" src=\"assets/images/spin.gif\">";
+// // document.getElementById("MED-LoadingValuesGif").style.display = 'block';
+//
+// // 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;
+//
+// // define two functions to manage the result received by the server
+// var success = function (responseText) {
+// // $%$ is used as delimeter (AnnotationName$%$[val1,...,valn])
+// var response = responseText.split("$%$");
+// if (response[0] != i2b2.MedCo.popup.latestAnnotationRequest){
+// // if I received an old response just ignore it
+// return
+// }
+//
+// var receivedValues = JSON.parse(response[1].slice(1, -1));
+// // load the annotation values in the popup
+// // var annotationValues = document.querySelector("#annotationValueList"); // don't use anymore the select
+// i2b2.MedCo.popup.annotationValues = [];
+// for(var i = 0; i < receivedValues.length; i++)
+// {
+// i2b2.MedCo.popup.annotationValues.push(receivedValues[i].toString());
+// // var opt = document.createElement("option");
+// // opt.value = receivedValues[i];
+// // opt.innerHTML = receivedValues[i];
+// // annotationValues.appendChild(opt);
+// }
+// // hide the loading gif
+// // document.getElementById("MED-LoadingValuesGif").style.display = 'none';
+// };
+// var error = function (err) {
+// alert("Error when trying to retrieve the values of the annotation from the database."+err)
+// };
+//
+// // 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);
+// }
+// };
+//
+// // get the selected annotation
+// var annotations = document.querySelector("#annotationList");
+// var selectedAnnotation = annotations.options[annotations.selectedIndex].value;
+// // store it so that I will know if the answer is the most recent
+// i2b2.MedCo.popup.latestAnnotationRequest = selectedAnnotation;
+//
+// req.open("GET", i2b2.MedCo.popup.getAnnotationValuesPath + "?annotation_name=" + selectedAnnotation , true);
+// req.send(null);
+// return req;
+// };
+//
+//
+// i2b2.MedCo.ctrlr.loadVariants = function (){
+// // 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;
+//
+// // define two functions to manage the result received by the server
+// var success = function (responseText) {
+// var response = JSON.parse(responseText);
+// for(var i=0; i<response.variants.length; i++)
+// {
+// i2b2.MedCo.model.panels[response.panel_number].push(response.variants[i]);
+// }
+// // I received the response so decrease the counter
+// i2b2.MedCo.popup.variantsQueryCounter -= 1;
+// };
+// var error = function (err) {
+// alert("Error when trying to retrieve the variants from the database."+err)
+// };
+//
+// // 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);
+// }
+// };
+//
+// // just write down that there is one more response we are waiting for
+// i2b2.MedCo.popup.variantsQueryCounter += 1;
+//
+// var annotations = document.querySelector("#annotationList");
+// var selectedAnnotation = annotations.options[annotations.selectedIndex].value;
+//
+// var selectedValue = document.querySelector("#selectedAnnotationValue").innerHTML;
+//
+// req.open("GET", i2b2.MedCo.popup.getVariantsPath +
+// "?annotation_name=" + selectedAnnotation +
+// "&annotation_value=" + selectedValue +
+// "&panel_number=" + i2b2.MedCo.popup.panelNumber, true);
+// req.send(null);
+// return req;
+// };
\ No newline at end of file