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R4897/js-i2b2/cells/plugins/MedCo/MedCo_ctrlr.js
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MedCo_ctrlr.js
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/***********************
* @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 (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 is an array all the (three) panels for easier access
i2b2.MedCo.model.panels = document.getElementsByClassName("medcoQryToolPanel");
for (i = 0 ; i < 3; i++){
i2b2.MedCo.model.panels[i].innerHTML = ""
}
// initialize empty parameter for the query (no panels content)
i2b2.MedCo.model.queryParameters = [[], [], []]; // three panels
// get the elements of the popup so to register an event handler to manage which annotations to display
i2b2.MedCo.model.chosenAnnotations = [[], [], []]; // in each panel there can be many annotations
searchBox = document.querySelector("#searchBox");
annotations = document.querySelector("#annotationList"); // this will be loaded with all the annotations
// just load fake annotations
for(i = 0; i < 1000; i++)
{
randAnnotation = Math.random().toString(36).substring(7);
var opt = document.createElement("option");
opt.value = randAnnotation;
opt.innerHTML = randAnnotation;
annotations.appendChild(opt);
}
// function to update the searchBox of the popup whenever a new key is entered
searchBox.addEventListener("keyup", function (e) {
var text = e.target.value;
var options = annotations.options;
for (var i = 0; i < options.length; i++) {
var option = options[i];
var optionText = option.text;
var lowerOptionText = optionText.toLowerCase();
var lowerText = text.toLowerCase();
var regex = new RegExp("^" + text, "i");
var match = optionText.match(regex);
if (match){ // if it starts the same the select this one
option.selected = true;
return;
}
var 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;
}
searchBox.selectedIndex = 0;
}
});
// query for metadata TODO
// load the secure ontology TODO
};
i2b2.MedCo.Unload = function() {
// purge old data
i2b2.MedCo.model = {};
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.queryParameters[nPanel].push(sdxData);
// show the info to the user
i2b2.MedCo.model.panels[nPanel].innerHTML += sdxData.sdxInfo.sdxDisplayName + "<br>";
// CHECK: some usefull functions:
// alert(i2b2.h.getXNodeVal(sdxData.origData.xmlOrig, "level"))
// alert(Object.getOwnPropertyNames(sdxData.origData));
// let the user know that the drop was successful by updating the content of the panel
// $("ExampTabs-PRSDROP").innerHTML = i2b2.h.Escape(sdxData.sdxInfo.sdxDisplayName);
// i2b2.MedCo.model.panels[nPanel].innerHTML = "";
// for (i = 0; i < i2b2.MedCo.model.queryParameters[nPanel].length; i++){
// i2b2.MedCo.model.panels[nPanel].innerHTML += i2b2.MedCo.model.queryParameters[nPanel][i].sdxInfo.sdxDisplayName + "<br>";
// };
// optimization to prevent requerying the hive for new results if the input dataset has not changed
// i2b2.ExampTabs.model.dirtyResultsData = true;
// alert(sdxData.sdxInfo.sdxDisplayName);
// 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.model.panels.length; i++){
i2b2.MedCo.model.panels[i].innerHTML = "";
};
i2b2.MedCo.model.queryParameters = [[], [], []];
};
i2b2.MedCo.ctrlr.run = function(){
};
// i2b2.MedCo.ctrlr.Encrypt = function (){
// // plain = DecryptInt("F43RC98qfZJp9ClCz4UY9PhZ/jSTnjbN6+K00rH7MEc3jrenGWZsnvv/PYbp3uAnW2Yh0cZQzs3+O76MT2Kt7w==", "U/MCDDfD63GSZiP26OrCU3HIkvqHdyReYV/vEk8oZQM=")
// // alert(plain)
// alert("")
// window.open('file:index.html')
// var exec = require('child_process').exec, child;
//
// child = exec('cat *.js bad_file | wc -l',
// function (error, stdout, stderr) {
// console.log('stdout: ' + stdout);
// console.log('stderr: ' + stderr);
// if (error !== null) {
// console.log('exec error: ' + error);
// }
// });
// child();
// }
// TODO
// i2b2.MedCo.ctrlr.runMetadataQuery = function(id) {
//
// // callback processor
// var scopedCallback = new i2b2_scopedCallback();
// scopedCallback.scope = this;
//
// // callback function (answer processing)
// scopedCallback.callback = function(results) {
//
// // check for errors
// if (results.error) {
// var responseHeader = i2b2.h.XPath(results.refXML, 'descendant::response_header')[0];
// if (responseHeader != undefined) {
// var status = i2b2.h.getXNodeVal(i2b2.h.XPath(responseHeader, "child::result_status")[0], 'status');
// if (status != "DONE") {
// alert("ERROR: Status not DONE in the received metadata.")
// //alert("Computation was not finished, partial results are available from query history");
// //var queryResult = i2b2.h.XPath(results.refXML, "descendant::*[local-name()='genomic_query_result']")[0];
// //i2b2.GEN.ctrlr.updateHistory(queryResult);
// } //else if (status == "NO_RECORDS") {
// //alert("No data for given query");
// //}
// } else {
// alert(results.refXML.getElementsByTagName('faultstring')[0].innerHTML);
// }
// } else {
// // extract data from response message and update model
// i2b2.MedCo.ctrlr.extractMetadataResult(results, id);
// i2b2.MedCo.ctrlr.updateMetadata(results.refXML);
// // Add to Previous Queries tab
// //i2b2.GEN.ctrlr.updateHistory(results.refXML);
// }
// // update the view results tab
// $$("DIV#GEN-mainDiv DIV#GEN-TABS DIV#GEN-CONTENT DIV#ResultTab".concat(id).concat(" DIV.progress"))[0].hide();
// }
//
// // AJAX CALL USING THE EXISTING CRC CELL COMMUNICATOR
// i2b2.GEN.ajax.plugin_GEN_Request("Plugin:GEN", {qname:i2b2.GEN.model.requestQueryName, pset:i2b2.GEN.model.requestPSet, query_definition:i2b2.GEN.model.requestQuery, query_type:i2b2.GEN.model.requestQueryType}, scopedCallback);
//
// };
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