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SecGene/webclient/GEN/GEN_ctrlr.js
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GEN_ctrlr.js
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/***********************
* @ProjectDescription Query on the genomic data and display results while preserving the privacy of the patients.
* @inherits i2b2
* @namespace i2b2.GEN
* @author
* @version 0.1
* --------------------------------------------------------------------------------------------------------------------
* This plugin is based on Tutorial plugin and examples on the webclient plugin development guide.
*/
i2b2.GEN.Init = function(loadedDiv) {
// setup model variables for this plugin
i2b2.GEN.model.responseXML = '';
i2b2.GEN.model.responseString = '';
i2b2.GEN.model.requestQuery = '';
i2b2.GEN.model.requestPSet = '';
i2b2.GEN.model.requestQueryType = '';
i2b2.GEN.model.requestQueryName = '';
i2b2.GEN.model.prsRecord = undefined;
i2b2.GEN.model.infoType = true;
i2b2.GEN.model.varType = true;
i2b2.GEN.view.tabId=0;
i2b2.sdx.Master.AttachType("gen-pset", "PRS", {dropTarget:true});
i2b2.sdx.Master.setHandlerCustom("gen-pset", "PRS", "DropHandler", i2b2.GEN.ctrlr.prsDropped);
// Add two more options to zygosity when genotypes are phased
if (i2b2.GEN.cfg.params['phase'] != 0) {
$('zygosity').add(new Option('Reference|Alternate', 'REFERENCE_ALTERNATE'));
$('zygosity').add(new Option('Alternate|Reference', 'ALTERNATE_REFERENCE'));
}
// manage YUI tabs
i2b2.GEN.view.yuiTabs = new YAHOO.widget.TabView("GEN-TABS", {activeIndex:0});
i2b2.GEN.view.yuiTabs.addListener('activeTabChange', function(e) {
var closeButton=' <div class="closeButton" onclick="JavaScript:i2b2.GEN.ctrlr.closeTab()"></div>';
e.prevValue.set('label', e.prevValue.get('label').replace(closeButton, ''));
if (i2b2.GEN.view.yuiTabs.getTabIndex(e.newValue) != 0 && i2b2.GEN.view.yuiTabs.getTabIndex(e.newValue) < i2b2.GEN.view.yuiTabs.get('tabs').length-2)
e.newValue.set('label', e.newValue.get('label').concat(closeButton));
else if (e.newValue.get('id') == "NEW-TAB") {
i2b2.GEN.ctrlr.addNewTab(false);
}
});
// Initialize parameters for result table
// Sort function for result table
// Based on the example of YUI2, http://yui.github.io/yui2/docs/yui_2.9.0_full/datatable/
var customSortFunction = function(a, b, desc, field) {
// Deal with empty values
if(!YAHOO.lang.isValue(a)) {
return (!YAHOO.lang.isValue(b)) ? 0 : 1;
} else if(!YAHOO.lang.isValue(b)) {
return -1;
}
// First compare by Column2
var comp = YAHOO.util.Sort.compare;
var compState = comp(a.getData(field), b.getData(field), desc);
// If values are equal, then compare by Column1
if (compState != 0)
return compState;
else {
compState = comp(a.getData("Chromosome"), b.getData("Chromosome"), desc);
if (compState != 0)
return compState;
else {
compState = comp(a.getData("Position"), b.getData("Position"), desc);
if (compState != 0)
return compState;
else {
compState = comp(a.getData("Alternate"), b.getData("Alternate"), desc);
return (compState != 0) ? compState : comp(a.getData("Result Type"), b.getData("Result Type"), desc);
}
}
}
}
i2b2.GEN.view.columnDefinition = [
{key:"Chromosome", resizeable:true, sortable:true, sortOptions: { sortFunction: customSortFunction }},
{key:"Position", resizeable:true, sortable:true, sortOptions: { sortFunction: customSortFunction }},
{key:"Reference", resizeable:true},
{key:"Alternate", resizeable:true},
{key:"Gene name", resizeable:true, sortable:true, sortOptions: { sortFunction: customSortFunction }},
{key:"dbSNP ID", resizeable:true, sortable:true, sortOptions: { sortFunction: customSortFunction }},
{key:"Result Type", resizeable:true, sortOptions: { sortFunction: customSortFunction }},
{key:"Result", resizeable:true, sortable:true, sortOptions: { sortFunction: customSortFunction }}
];
i2b2.GEN.view.data = {};
i2b2.GEN.view.ds = {};
i2b2.GEN.view.dataTable = {};
i2b2.GEN.view.responseSchemaFields = [{key:"Chromosome", parser:"number"},
{key:"Position", parser:"number"},
{key:"Reference"},
{key:"Alternate"},
{key:"Gene name"},
{key:"dbSNP ID"},
{key:"Result Type"},
{key:"Result", parser:"number"}
];
i2b2.GEN.view.resultTypes = {MUTATION_COUNT:'MUTATION_COUNT',
HOMOZYGOUS_REFERENCE_COUNT:'HOMOZYGOUS_REFERENCE_COUNT',
HOMOZYGOUS_ALTERNATE_COUNT:'HOMOZYGOUS_ALTERNATE_COUNT',
HETEROZYGOUS_COUNT:'HETEROZYGOUS_COUNT',
REFERENCE_ALTERNATE_COUNT:'REFERENCE_ALTERNATE_COUNT',
ALTERNATE_REFERENCE_COUNT:'ALTERNATE_REFERENCE_COUNT',
HOMOZYGOUS_REFERENCE_FREQUENCY:'HOMOZYGOUS_REFERENCE_FREQUENCY',
HOMOZYGOUS_ALTERNATE_FREQUENCY:'HOMOZYGOUS_ALTERNATE_FREQUENCY',
HETEROZYGOUS_FREQUENCY:'HETEROZYGOUS_FREQUENCY',
REFERENCE_ALTERNATE_FREQUENCY:'REFERENCE_ALTERNATE_FREQUENCY',
ALTERNATE_REFERENCE_FREQUENCY:'ALTERNATE_REFERENCE_FREQUENCY',
ALLELE_FREQUENCY:'ALTERNATE_AF'};
};
i2b2.GEN.Unload = function() {
// purge old data
i2b2.GEN.model = {};
i2b2.GEN.view = {};
try { i2b2.GEN.yuiPanel.destroy(); } catch(e) {}
return true;
};
i2b2.GEN.ctrlr.changeQueryTab = function(v) {
if (v == 1) {
i2b2.GEN.model.infoType=true;
$('byVariant').hide();
$('byGene').show();
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].checked=false;
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].enable();
} else {
i2b2.GEN.model.infoType=false;
$('byGene').hide();
$('byVariant').show();
if (!i2b2.GEN.model.varType && $('zygosity').value != "") {
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].enable();
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].checked=false;
} else {
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].checked=false;
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].enable();
}
}
}
i2b2.GEN.ctrlr.changeVariantView = function(v) {
if (v == 1) {
i2b2.GEN.model.varType=true;
$('rs_input').disabled = false;
$('loc_input').disabled = true;
$('zygosity').disabled = true;
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].checked=false;
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].enable();
} else {
i2b2.GEN.model.varType=false;
$('rs_input').disabled = true;
$('loc_input').disabled = false;
$('zygosity').disabled = false;
if ($('zygosity').value == "") {
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].checked=false;
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].enable();
} else {
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].enable();
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].checked=false;
}
}
}
i2b2.GEN.ctrlr.updateResultType = function() {
if ($('zygosity').value == "") {
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].enable();
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].checked=false;
} else {
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=ALLELE_FREQUENCY][type=checkbox]')[0].checked=false;
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].enable();
}
}
i2b2.GEN.ctrlr.clear = function() {
$('gene_input').value="";
$('rs_input').value="";
$('loc_input').value="";
$('zygosity').selectedIndex=0;
//$$('DIV.GEN-ResultTypes input[value=COUNT][type=checkbox]')[0].checked = true;
$$('DIV.GEN-ResultTypes input[value!=FREQUENCY][type=checkbox]').forEach(function(v) {v.checked = false; v.enable();});
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].disable();
$$('DIV.GEN-ResultTypes input[value=FREQUENCY][type=checkbox]')[0].checked=false;
i2b2.GEN.model.prsRecord = undefined;
$('gen-pset').innerHTML = "Drop a Patient Set";
}
i2b2.GEN.ctrlr.closeTab = function() {
var target = i2b2.GEN.view.yuiTabs.get('activeTab');
var id = target.id;
i2b2.GEN.view.data[id] = null;
delete i2b2.GEN.view.data[id];
i2b2.GEN.view.ds[id] = null;
delete i2b2.GEN.view.ds[id];
i2b2.GEN.view.dataTable[id].destroy();
delete i2b2.GEN.view.dataTable[id];
var index = i2b2.GEN.view.yuiTabs.getTabIndex(target);
if (index == i2b2.GEN.view.yuiTabs.get('tabs').length-3)
index--;
i2b2.GEN.view.yuiTabs.selectTab(index);
i2b2.GEN.view.yuiTabs.removeTab(target);
}
i2b2.GEN.ctrlr.isValidQuery = function() {
if (i2b2.GEN.model.infoType) {
return $('gene_input').value.trim().split(/\r*\n*\s*(?:,|;)\s*/).filter(Boolean).length>0;
} else if (i2b2.GEN.model.varType) {
return $('rs_input').value.trim().split(/\r*\n*\s*(?:,|;)\s*/).filter(Boolean).length>0;
} else {
var locs = $('loc_input').value.trim().toUpperCase().split(/\r*\n*\s*(?:,|;)\s*/).filter(Boolean);
return (locs.length > 0) ? locs.reduce( function(prev, curr) { return prev | curr.match(/^(CHR){0,1}[0-9]+(\s*:\s*[0-9]+(\s*-\s*[0-9]+){0,1}\s*([ACGT]+\s*>\s*[ACGT]+){0,1}){0,1}$/g) != null}, false) : false;
}
}
i2b2.GEN.ctrlr.run = function() {
if (i2b2.GEN.ctrlr.isValidQuery()) {
var resType = $$('DIV.GEN-ResultTypes input[name=queryType][type=checkbox]:checked:enabled');
if (resType.length>0) {
//remove old results
i2b2.GEN.model.responseXML = '';
i2b2.GEN.model.responseString = '';
i2b2.GEN.model.requestQuery = '';
i2b2.GEN.model.requestPSet = '';
i2b2.GEN.model.requestQueryType = '';
i2b2.GEN.model.requestQueryName = '';
var date = new Date();
var queryNamePostfix = '@'.concat(date.getHours()).concat(':').concat(date.getMinutes()).concat(':').concat(date.getSeconds())
resType.forEach(function(v,i) {resType[i]=v.value;})
// When query by variant and one of zygosity is chosen
if (!i2b2.GEN.model.infoType && !i2b2.GEN.model.varType && $('zygosity').value != "") {
if (resType.indexOf('MUTATION_COUNT') != -1) {
resType[resType.indexOf('MUTATION_COUNT')]=$('zygosity').value.concat('_COUNT');
}
if (resType.indexOf('FREQUENCY') != -1) {
resType[resType.indexOf('FREQUENCY')]=$('zygosity').value.concat('_FREQUENCY');
}
}
i2b2.GEN.model.requestQueryType = '\t\t<genomic_query_type>'.concat(resType.join('</genomic_query_type>\n\t\t<genomic_query_type>')).concat('</genomic_query_type>');
if (i2b2.GEN.model.prsRecord) {
i2b2.GEN.model.requestPSet = i2b2.GEN.model.prsRecord.sdxInfo.sdxKeyValue;
}
if (i2b2.GEN.model.infoType) {
i2b2.GEN.model.requestQueryName = $('gene_input').value.trim().slice(0,30).concat(queryNamePostfix);
i2b2.GEN.model.requestQuery = '\t\t<query_info>\n\t\t\t<gene_name>'
.concat($('gene_input').value.trim().toUpperCase().split(/\r*\n*\s*(?:,|;)\s*/g).filter(Boolean).join('</gene_name>\n\t\t</query_info>\n\t\t<query_info>\n\t\t\t<gene_name>'))
.concat('</gene_name>\n\t\t</query_info>');
} else if (i2b2.GEN.model.varType) {
i2b2.GEN.model.requestQueryName = $('rs_input').value.trim().slice(0,30).concat(queryNamePostfix);
i2b2.GEN.model.requestQuery = '\t\t<query_info>\n\t\t\t<rs_number>'
.concat($('rs_input').value.trim().toUpperCase().split(/\r*\n*\s*(?:,|;)\s*/g).filter(Boolean).join('</rs_number>\n\t\t</query_info>\n\t\t<query_info>\n\t\t\t<rs_number>'))
.concat('</rs_number>\n\t\t</query_info>');
} else {
i2b2.GEN.model.requestQueryName = $('loc_input').value.trim().slice(0,30).concat(queryNamePostfix);
var locus = $('loc_input').value.trim().toUpperCase().split(/\r*\n*\s*(?:,|;)\s*/);
var interpret = function(str) {
var res = [];
if (str = str.match(/^(?:CHR){0,1}([0-9]+)(?:\s*:\s*([0-9]+(?:\s*-\s*[0-9]+){0,1})\s*(?:([ACGT]+)\s*>\s*([ACGT]+)){0,1}){0,1}$/)) {
res.push('\t\t<query_info>\n\t\t\t<chromosome>');
res.push(str[1]);
res.push('</chromosome>\n');
if (str[2]) {
res.push('\t\t\t<position>');
res.push(str[2]);
res.push('</position>\n');
}
if (str[3]) {
res.push('\t\t\t<reference>');
res.push(str[3]);
res.push('</reference>\n\t\t\t<alternate>');
res.push(str[4]);
res.push('</alternate>\n');
}
res.push('\t\t</query_info>\n');
}
return res.join('');
}
locus.forEach(function(v,i) { locus[i]=interpret(v); });
i2b2.GEN.model.requestQuery = locus.join('');
}
var id = i2b2.GEN.ctrlr.addNewTab(true);
$$("DIV#GEN-mainDiv DIV#GEN-TABS DIV#GEN-CONTENT DIV#ResultTab".concat(id).concat(" DIV.progress"))[0].show();
// give a brief pause for the GUI to catch up
setTimeout(i2b2.GEN.ctrlr.runGenomicQuery, 50, id);
} else {
alert('At least one type of query should be selected');
}
} else {
alert('Please provide any query information');
}
};
i2b2.GEN.ctrlr.addNewTab = function(withQueryDefinition) {
var id = i2b2.GEN.view.tabId;
i2b2.GEN.view.tabId++;
var tab = new YAHOO.widget.Tab({
label: 'Query Result #'.concat(id),
content: '<div id="ResultTab'.concat(id).concat('" class="GEN-MainContent"><div class="GEN-MainContentPad"><h2>Query Definition</h2>').concat(withQueryDefinition ? ((i2b2.GEN.model.infoType) ? ('<div class="label3">Gene Name</div>'.concat($('gene_input').value.trim()).concat('<br style="clear:both" />')) : (i2b2.GEN.model.varType) ? ('<div class="label3">dbSNP ID</div>'.concat($('rs_input').value.trim()).concat('<br style="clear:both" />')) : ('<div class="label3">Location</div>'.concat($('loc_input').value.trim()).concat('<br style="clear:both" /><div class="label3">Zygosity</div>').concat($('zygosity').selectedOptions[0].innerHTML).concat('<br style="clear:both" />'))) : '').concat('<hr noshade="" size="1"><h2>Result</h2><div class="progress" style="display:none;"><div class="loading"></div> Query is in progress</div><div class="dropresult" id="gen-history').concat(id).concat('">Drop a Query Result to append to table</div><div id="GEN-ResultTable').concat(id).concat('"></div></div></div>')
});
tab.id = id;
i2b2.GEN.view.yuiTabs.addTab(tab, i2b2.GEN.view.yuiTabs.get('tabs').length-2);
i2b2.GEN.view.yuiTabs.selectTab(i2b2.GEN.view.yuiTabs.get('tabs').length-3);
i2b2.sdx.Master.AttachType("gen-history".concat(id), "QM", {dropTarget:true});
i2b2.sdx.Master.setHandlerCustom("gen-history".concat(id), "QM", "DropHandler", i2b2.GEN.ctrlr.runHistoryQuery);
i2b2.GEN.view.data[id] = [];
i2b2.GEN.view.ds[id] = new YAHOO.util.DataSource(i2b2.GEN.view.data[id]);
i2b2.GEN.view.ds[id].responseType = YAHOO.util.DataSource.TYPE_JSARRAY;
i2b2.GEN.view.ds[id].responseSchema = {
fields:i2b2.GEN.view.responseSchemaFields
};
i2b2.GEN.view.dataTable[id] = new YAHOO.widget.DataTable("GEN-ResultTable".concat(id), i2b2.GEN.view.columnDefinition, i2b2.GEN.view.ds[id])
return id;
}
i2b2.GEN.ctrlr.updateHistory = function(refXML) {
// Brought from Refresh function of CRC_ctrlr_History.js in order to keep same structure of history object
var queryResult = i2b2.h.XPath(refXML, "descendant::*[local-name()='genomic_query_result']")[0];
var o = new Object;
o.id = i2b2.h.getXNodeVal(queryResult,'query_master_id');
o.realname = i2b2.h.getXNodeVal(queryResult,'query_name');
o.userid = i2b2.h.getXNodeVal(refXML, 'username');
o.group = i2b2.h.getXNodeVal(refXML, 'project_id');
o.created = i2b2.h.getXNodeVal(queryResult,'create_date');
var dStr = '';
var d = o.created.match(/^[0-9\-]*/).toString();
if (d) {
d = d.replace(/-/g,'/');
d = new Date(Date.parse(d));
if (d) {
dStr = ' [' + (d.getMonth()+1) + '-' + d.getDate() + '-' + d.getFullYear().toString() + ']';
}
}
o.name = o.realname + dStr + ' ['+o.userid+']';
// encapsulate into an SDX package
var sdxDataPack = i2b2.sdx.Master.EncapsulateData('QM',o);
// save the node to the CRC data model
i2b2.sdx.Master.Save(sdxDataPack, null);
// Broadcast an update event letting interested view controllers know that the Categories data model has been updated
var DataUpdateSignal = {
DataLocation: "i2b2.CRC.model.QueryMasters",
DataRef: i2b2.CRC.model.QueryMasters
}
i2b2.CRC.ctrlr.history.events.onDataUpdate.fire(DataUpdateSignal);
}
// i2b2.GEN.ctrlr.extractResult = function(results, id) {
// i2b2.GEN.model.responseXML = results.refXML;
// i2b2.GEN.model.res = results;
// var columns = ["chromosome", "position", "reference", "alternate", "gene_name", "rs_number"];
// var csParameter = i2b2.h.XPath(results.refXML, "descendant::*[local-name()='cryptosystem_parameter']");
// if (csParameter.length > 0) {
// // Assuming cofficient is smaller than 64 bits
// i2b2.GEN.model.coefficientModulus = bigInt(i2b2.h.getXNodeVal(csParameter[0], "coefficient_modulus"));
// i2b2.GEN.model.plaintextModulus = bigInt(i2b2.h.getXNodeVal(csParameter[0], "plaintext_modulus"));
// i2b2.GEN.model.polynomialDegree = parseInt(i2b2.h.getXNodeVal(csParameter[0], "polynomial_degree"));
// }
// var queryResult = i2b2.h.XPath(results.refXML, "descendant::*[local-name()='genomic_query_result']")[0];
// var queryResultInstance = i2b2.h.XPath(queryResult, "child::genomic_query_result_instance");
// for (var i=0;i<queryResultInstance.length;i++) {
// var qri = queryResultInstance[i];
// var ct = [].map.call( qri.getElementsByTagName("ciphertext"), function(node){return node.textContent});
// if (ct.length > 0) {
// var pkid = queryResult.getElementsByTagName('partialkey_id')[0].textContent;
// if (i2b2.GEN.model.partialkeyId != pkid) {
// i2b2.GEN.model.partialkeyId = pkid;
// // Get partialkey from proxy i2b2.GEN.model.partialkey
// var req = new XMLHttpRequest();
// var t = new Template(i2b2.GEN.cfg.msgs.plugin_GEN_PROXY_Request, /(^|.|\r|\n)(\{{{\s*(\w+)\s*}}})/);
// req.open('POST', i2b2.GEN.cfg.cellParams['proxy'].concat('handlePartialKeyRequest'), false);
// req.setRequestHeader('Content-Type', 'text/xml');
// req.send(t.evaluate({id:i2b2.GEN.model.partialkeyId}));
// if (req.status == 200) {
// i2b2.GEN.model.proxyResponseXML = req.responseXML;
// var pk = i2b2.h.XPath(req.responseXML, "descendant::*[local-name()='partial_key']");
// if (pk.length >0) {
// var kv = i2b2.h.XPath(pk[0], "child::value");
// if (kv.length > 0) {
// kv.forEach(function(v,i) { kv[i]=v.firstChild.nodeValue; });
// i2b2.GEN.model.partialkey = kv;
// } else {
// i2b2.GEN.model.partialkey = undefined;
// }
// }
// } else {
// i2b2.GEN.model.partialkey = undefined;
// alert("Cannot connect to Proxy/key management");
// }
// }
// // Decrypt result if key exists
// if (i2b2.GEN.model.partialkey != undefined) {
// var resultType = qri.getElementsByTagName("genomic_query_type")[0].textContent;
// var queryInformation = qri.getElementsByTagName("genomic_result_info");
// for (var j=0;j<queryInformation.length;j++) {
// var qi = queryInformation[j];
// var v = {};
// for (var k=0;k<columns.length-1;k++) {
// var temp = qi.getElementsByTagName(columns[k])[0];
// if (temp != undefined)
// v[i2b2.GEN.view.ds[id].responseSchema.fields[k].key] = temp.textContent;
// }
// var rs=qi.getElementsByTagName(columns[k])[0];
// if (rs != undefined)
// rs = rs.textContent.toLowerCase();
// v[i2b2.GEN.view.ds[id].responseSchema.fields[k].key] = rs;
// v['Result Type'] = i2b2.GEN.view.resultTypes[resultType];
// if (resultType.endsWith('FREQUENCY')) {
// var count = qri.getElementsByTagName("count")[0].textContent;
// var result = (i2b2.GEN.ctrlr.decryptOneDegree(qi.getElementsByTagName("encrypted_value")[0].textContent, ct, i2b2.GEN.model.partialkey, i2b2.GEN.model.polynomialDegree, i2b2.GEN.model.plaintextModulus, i2b2.GEN.model.coefficientModulus, parseInt(qi.getElementsByTagName("degree")[0].textContent))/count).toFixed(6);
// v.Result = (result >= 0.0 && result <= 1.0) ? result : 0.0;
// } else {
// var result = i2b2.GEN.ctrlr.decryptOneDegree(qi.getElementsByTagName("encrypted_value")[0].textContent, ct, i2b2.GEN.model.partialkey, i2b2.GEN.model.polynomialDegree, i2b2.GEN.model.plaintextModulus, i2b2.GEN.model.coefficientModulus, parseInt(qi.getElementsByTagName("degree")[0].textContent));
// v.Result = (result >= 0 && result <= 0.9*i2b2.GEN.model.plaintextModulus) ? result : 0;
// }
// i2b2.GEN.view.data[id].push(v);
// }
// } else {
// // Failed to get partial key
// }
// } else {
// // List of failed variants
// }
// }
// i2b2.GEN.view.ds[id].sendRequest(null, {success: i2b2.GEN.view.dataTable[id].onDataReturnInitializeTable}, i2b2.GEN.view.dataTable[id]);
// i2b2.GEN.view.dataTable[id].sortColumn(i2b2.GEN.view.dataTable[id].getColumn(0), 'asc');
// }
i2b2.GEN.ctrlr.extractResult = function(results, id) {
i2b2.GEN.model.responseXML = results.refXML;
i2b2.GEN.model.res = results;
var columns = ["chromosome", "position", "reference", "alternate", "gene_name", "rs_number"];
results.refXML.getElementsByTagName('security')[0].remove();
results.refXML.getElementsByTagName('message_control_id')[0].getElementsByTagName('instance_num')[0].textContent++;
results.refXML.getElementsByTagName('response_header')[0].remove();
var queryResult = i2b2.h.XPath(results.refXML, "descendant::*[local-name()='genomic_query_result']")[0];
var queryResultInstance = queryResult.getElementsByTagName('genomic_query_result_instance');
var queryResultVariantInformation = [];
var csParameter = queryResult.getElementsByTagName('cryptosystem_parameter');
if (csParameter.length > 0) {
// Assuming cofficient is smaller than 64 bits
i2b2.GEN.model.coefficientModulus = bigInt(csParameter[0].getElementsByTagName('coefficient_modulus')[0].textContent);
i2b2.GEN.model.plaintextModulus = bigInt(csParameter[0].getElementsByTagName('plaintext_modulus')[0].textContent);
csParameter[0].getElementsByTagName('plaintext_modulus')[0].remove();
i2b2.GEN.model.polynomialDegree = parseInt(csParameter[0].getElementsByTagName('polynomial_degree')[0].textContent);
}
for (var i=0;i<queryResultInstance.length;i++) {
var qri = queryResultInstance[i];
queryResultVariantInformation[i]={};
queryResultVariantInformation[i].qt = qri.getElementsByTagName('genomic_query_type')[0];
queryResultVariantInformation[i].qt.remove();
queryResultVariantInformation[i].count = qri.getElementsByTagName('count')[0];
queryResultVariantInformation[i].count.remove();
queryResultVariantInformation[i].info = [].slice.call(qri.getElementsByTagName('genomic_result_info'));
for (var j=0;j<queryResultVariantInformation[i].info.length;j++) {
queryResultVariantInformation[i].info[j].remove();
}
}
var req = new XMLHttpRequest();
req.open('POST', i2b2.GEN.cfg.cellParams['proxy'].concat('handleDecryptionRequest'), false);
req.setRequestHeader('Content-Type', 'text/xml');
req.send(results.refXML);
if (req.status == 200) {
i2b2.GEN.model.proxyResponseXML = req.responseXML;
queryResult = i2b2.h.XPath(req.responseXML, "descendant::*[local-name()='genomic_query_result']")[0];
queryResultInstance = queryResult.getElementsByTagName('genomic_query_result_instance');
for (var i=0;i<queryResultVariantInformation.length;i++) {
var qri = queryResultInstance[i];
var ct = [].map.call( qri.getElementsByTagName("ciphertext"), function(node){return node.textContent});
var denominator = [].map.call( qri.getElementsByTagName("denominator"), function(node){return node.textContent});
for (var j=0;j<queryResultVariantInformation[i].info.length;j++) {
var qi = queryResultVariantInformation[i].info[j];
var v = {};
for (var k=0;k<columns.length-1;k++) {
var temp = qi.getElementsByTagName(columns[k])[0];
if (temp != undefined)
v[i2b2.GEN.view.ds[id].responseSchema.fields[k].key] = temp.textContent;
}
var rs=qi.getElementsByTagName(columns[k])[0];
if (rs != undefined)
rs = rs.textContent.toLowerCase();
v[i2b2.GEN.view.ds[id].responseSchema.fields[k].key] = rs;
v['Result Type'] = i2b2.GEN.view.resultTypes[queryResultVariantInformation[i].qt.textContent];
if (v['Result Type'].endsWith('FREQUENCY') || v['Result Type'].endsWith('AF')) {
if(denominator.length==0) {
var result = (i2b2.GEN.ctrlr.decryptOneDegree(qi.getElementsByTagName("encrypted_value")[0].textContent, ct[parseInt(qi.getElementsByTagName("degree")[0].textContent)], i2b2.GEN.model.partialkey, i2b2.GEN.model.polynomialDegree, i2b2.GEN.model.plaintextModulus, i2b2.GEN.model.coefficientModulus)/queryResultVariantInformation[i].count.textContent).toFixed(6);
v.Result = (result >= 0.0 && result <= 1.0) ? result : 0.0;
}else {
var result = i2b2.GEN.ctrlr.decryptOneDegree(qi.getElementsByTagName("encrypted_value_denominator")[0].textContent, denominator[parseInt(qi.getElementsByTagName("degree")[0].textContent)], i2b2.GEN.model.partialkey, i2b2.GEN.model.polynomialDegree, i2b2.GEN.model.plaintextModulus, i2b2.GEN.model.coefficientModulus);
result = (i2b2.GEN.ctrlr.decryptOneDegree(qi.getElementsByTagName("encrypted_value")[0].textContent, ct[parseInt(qi.getElementsByTagName("degree")[0].textContent)], i2b2.GEN.model.partialkey, i2b2.GEN.model.polynomialDegree, i2b2.GEN.model.plaintextModulus, i2b2.GEN.model.coefficientModulus)/result).toFixed(6);
v.Result = (result >= 0.0 && result <= 1.0) ? result : 0.0;
}
} else {
var result = i2b2.GEN.ctrlr.decryptOneDegree(qi.getElementsByTagName("encrypted_value")[0].textContent, ct[parseInt(qi.getElementsByTagName("degree")[0].textContent)], i2b2.GEN.model.partialkey, i2b2.GEN.model.polynomialDegree, i2b2.GEN.model.plaintextModulus, i2b2.GEN.model.coefficientModulus);
v.Result = (result >= 0 && result <= 0.9*i2b2.GEN.model.plaintextModulus) ? result : 0;
}
i2b2.GEN.view.data[id].push(v);
}
}
i2b2.GEN.view.ds[id].sendRequest(null, {success: i2b2.GEN.view.dataTable[id].onDataReturnInitializeTable}, i2b2.GEN.view.dataTable[id]);
i2b2.GEN.view.dataTable[id].sortColumn(i2b2.GEN.view.dataTable[id].getColumn(0), 'asc');
} else {
i2b2.GEN.model.partialkey = undefined;
alert("Cannot connect to Proxy/key management");
}
}
i2b2.GEN.ctrlr.runGenomicQuery = function(id) {
// callback processor
var scopedCallback = new i2b2_scopedCallback();
scopedCallback.scope = this;
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 == "NOT_FINISHED") {
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.GEN.ctrlr.extractResult(results, id);
// Add to Previous Queries tab
i2b2.GEN.ctrlr.updateHistory(results.refXML);
}
// update the view results tab
$$("DIV#GEN-mainDiv DIV#GEN-TABS DIV#GEN-CONTENT DIV#ResultTab".concat(id).concat(" DIV.progress"))[0].hide();
}
// AJAX CALL USING THE EXISTING CRC CELL COMMUNICATOR
i2b2.GEN.ajax.plugin_GEN_Request("Plugin:GEN", {qname:i2b2.GEN.model.requestQueryName, pset:i2b2.GEN.model.requestPSet, query_definition:i2b2.GEN.model.requestQuery, query_type:i2b2.GEN.model.requestQueryType}, scopedCallback);
};
i2b2.GEN.ctrlr.runHistoryQuery = function(sdxData) {
sdxData = sdxData[0];
var id = i2b2.GEN.view.yuiTabs.get('activeTab').id;
var scopedCallback = new i2b2_scopedCallback();
scopedCallback.scope = this;
scopedCallback.callback = function(results) {
if (results.error) {
var responseHeader = i2b2.h.XPath(results.refXML, 'descendant::response_header')[0];
if (responseHeader != undefined) {
var status = i2b2.h.getXNodeVal(i2b2.h.XPath(responseHeader, "child::result_status")[0], 'status');
if (status == "NO_RESULT") {
alert("Given result is not a genomic query result");
}
} else {
alert(results.refXML.getElementsByTagName('faultstring')[0].innerHTML);
}
} else {
i2b2.GEN.ctrlr.extractResult(results, id);
}
$$("DIV#GEN-mainDiv DIV#GEN-TABS DIV#GEN-CONTENT DIV#ResultTab".concat(id).concat(" DIV.progress"))[0].hide();
}
$$("DIV#GEN-mainDiv DIV#GEN-TABS DIV#GEN-CONTENT DIV#ResultTab".concat(id).concat(" DIV.progress"))[0].show();
i2b2.GEN.ajax.plugin_GEN_History("Plugin:GEN", {query_master_id:sdxData.origData.id, query_name:sdxData.origData.realname, create_date:sdxData.origData.created}, scopedCallback);
}
// Brought from webclient plugin example
i2b2.GEN.ctrlr.prsDropped = function(sdxData) {
sdxData = sdxData[0]; // only interested in first record
// save the info to our local data model
i2b2.GEN.model.prsRecord = sdxData;
// let the user know that the drop was successful by displaying the name of the patient set
$('gen-pset').innerHTML = i2b2.h.Escape(sdxData.sdxInfo.sdxDisplayName);
// temporarly change background color to give GUI feedback of a successful drop occuring
$('gen-pset').style.background = "#CFB";
setTimeout("$('gen-pset').style.background='#DEEBEF'", 250);
// optimization to prevent requerying the hive for new results if the input dataset has not changed
// i2b2.ExampPDO.model.dirtyResultsData = true;
};
i2b2.GEN.ctrlr.prsClicked = function() {
i2b2.GEN.model.prsRecord = undefined;
$('gen-pset').innerHTML = "Drop a Patient Set";
$('gen-pset').style.background = "#CFB";
setTimeout("$('gen-pset').style.background='#DEEBEF'", 250);
}
//DEC(c0,c1) = round(t/q * ((c0 + c1 * s) mod q)) mod t
i2b2.GEN.ctrlr.decrypt = function(c,s,d,t,q){
var convReduceAddMod = function(a1,a2,a3,d,q) {
var res =[];
for (var i=0;i<d;i++) {
var sum=bigInt(0);
for (var j=0;j<d;j++) {
if (j > i) {
sum=sum.subtract(bigInt(a1[j]).multiply(bigInt(a2[(d-j+i)%d])).mod(q));
} else {
sum=sum.add(bigInt(a1[j]).multiply(bigInt(a2[(d-j+i)%d])).mod(q));
}
}
res.push(sum.add(bigInt(a3[i])).mod(q).add(q).mod(q));
}
return res;
}
//((c0 + c1 * s) mod q)
var mult_step=convReduceAddMod(c.slice(d,2*d), s, c.slice(0,d), d, q);
//round((t*X)/q)
var res=[];
for (var i=0;i<mult_step.length;i++){
var v=mult_step[i].multiply(t);
res.push(v.divide(q).add(v.mod(q).multiply(2).divide(q)).toString());
}
return res;
}
// i2b2.GEN.ctrlr.decryptOneDegree = function(v,c,s,d,t,q,p) {
// var sum=bigInt(0);
// for (var i=0;i<d;i++) {
// if (i > p) {
// sum=sum.subtract(bigInt(c[i]).multiply(bigInt(s[(d-i+p)])));
// } else {
// sum=sum.add(bigInt(c[i]).multiply(bigInt(s[p-i])));
// }
// }
// var v=sum.add(bigInt(v)).mod(q);
// if (v < 0)
// v=v.add(q);
// v=v.multiply(t);
// v=v.divmod(q);
// if (v.remainder.multiply(2) >= q)
// v.quotient=v.quotient.add(1);
// return v.quotient.mod(t).toString();
// }
i2b2.GEN.ctrlr.decryptOneDegree = function(v,c,s,d,t,q) {
var sum=bigInt(c);
var v=sum.add(bigInt(v)).mod(q);
v=v.multiply(t);
v=v.divmod(q);
if (v.remainder.multiply(2) >= q)
v.quotient=v.quotient.add(1);
return v.quotient.mod(t).toString();
}
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