diff --git a/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_tests.js b/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_tests.js index a8b9463a6..a762be826 100644 --- a/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_tests.js +++ b/shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/MedCo_tests.js @@ -1,314 +1,314 @@ -i2b2.MedCo.test = {} +i2b2.MedCo.test = {}; // questions: always select all zygosity options? var cutaneous_melanoma = ["2"]; // (25 variants): var braf_gene = ["-7054948997223410688", "-7054948998062267136", "-7054968999892742144", "-7054948999337337856", "-7054948997064022784", "-7054953138544961536", "-7054948997064020736", "-7054923607457132544", "-7054904773018905600", "-7054898625779855360", "-7054948987408734208", "-7054923379857424384", "-7054917142457610240", "-7054861692282335232", "-7054948050082458624", "-7054922546600210432", "-7054949048695910400", "-7054923381098933248", "-7054861517262417920", "-7054918645662608384", "-7054905185268658176", "-7054904954414166016", "-7054898626853597184", "-7054904932905773056", "-7054861823278837760"]; // (58 variants) var protein_600 = ["-8933802084025738584", "-6486664075878068224", "-5631356589790194688", "-3744382902155078656", "-4243330163464466432", "-8390864270639754240", "-2861998644146466816", "-8933794510723345408", "-2275778788769918976", "-3744380364936704000", "-4847903122799977472", "-3744370070973837312", "-6486663046126103552", "-2862005101596240896", "-8933793458456358912", "-3731886507003209728", "-4243326752186690560", "-3684888714590289920", "-6600247701843995648", "-5707938912580661248", "-6600348525161082880", "-4243327620843826176", "-5707936738253467648", "-3744381594337537024", "-8390871813676067840", "-6486638321073122304", "-8718336899686591488", "-8161767032237320192", "-8718388095730315264", "-6600348471507544064", "-4847902555864297472", "-8718385496201359360", "-3744381715771026432", "-8390900435338128384", "-4243331029974117376", "-8718385510160003072", "-5707941003155992576", "-5707940965541473280", "-3744377054557105152", "-8390878215358377984", "-8161775324644764672", "-8161760075430494208", "-8933792699320889344", "-8933788672755493888", "-8718360110998468096", "-5707941120160295936", "-6600276494231006208", "-8933788638429310976", "-6486653465127809024", "-3744380416476311552", "-3729075172548795136", "-6600294904608320512", "-8933788867136319488", "-5707939282988035072", "-3744381760767524864", "-2275781595497491456", "-8933793225454383104", "-4243329794097277952"]; // (14 variants) var pten_gene = ["-6244734599302213632", "-6244835122005142528", "-6244734615609652992", "-6244731379150482432", "-6244761261385445376", "-6244761331212216320", "-6244803225329855488", "-6244761257090477056", "-6244761165822422016", "-6244761148709661696", "-6244761290443582464", "-6244734719527742464", "-6244803244478955520", "-6244731450050998272"]; // (22 variants) var cdkn2a_gene = ["-6605707269956960256", "-6605707340823916544", "-6605707363372498944", "-6605707399913269248", "-6605707450345581568", "-6605707366560164864", "-6605707493295259648", "-6605707451419324416", "-6605707339750174720", "-6605707347467692032", "-6605707487054123520", "-6605707304132149248", "-6605703514008055808", "-6605707366560165888", "-6605707438500867072", "-6605707503026037760", "-6605703519225765120", "-6605707607111888896", "-6605707340672917504", "-6605703519376764928", "-6605707351594886144", "-6605707619996790784"]; // (9 variants) var map2k1_gene = ["-4828214681296432128", "-4828266596713621504", "-4828266483970731008", "-4828258079793473536", "-4828266501150601216", "-4828266502224342016", "-4828257969198066688", "-4828266574613577728", "-4828218249340513280"]; // (7 variants) var mpa2k2 = ["-3742593253707344896", "-3742593391179853824", "-3742595392634613760", "-3742581279372079104", "-3742593229011282944", "-3742591331743035392", "-3742581136564416512"]; // simple test query var queryTest = [ [{"sensitive": true, "values": cutaneous_melanoma}] ] // Query A: // -panel 1: // cutaneous_melanoma // -panel 2: // braf_gene // -panel 3: // protein_600 var queryA = [ [{"sensitive": true, "values": cutaneous_melanoma}], [{"sensitive": true, "values": braf_gene}], [{"sensitive": true, "values": protein_600}] ]; // Query B: // -panel 1: // cutaneous_melanoma // -panel 2: // braf_gene // -panel 3: // pten_gene, cdkn2a_gene, map2k1_gene, mpa2k2 var queryB = [ [{"sensitive": true, "values": cutaneous_melanoma}], [{"sensitive": true, "values": braf_gene}], [{"sensitive": true, "values": pten_gene}, {"sensitive": true, "values": cdkn2a_gene}, {"sensitive": true, "values": map2k1_gene}, {"sensitive": true, "values": mpa2k2}] ]; i2b2.MedCo.test.ctrlr = { // time the action started startTime: null, // whether the query has been encrypted encrypted: false, // whether it is already doing something (encrypting or sending the queries) doing: false, // pointer to the interval object so to stop it timeinterval: null, // response of the query response: null, encrypt: function(){ if (this.doing){ alert("Already doing something.") return } this.doing = true; var startTime = new Date().getTime(); var query = this.getQuery(); // clear encryption cache and start encryption i2b2.MedCo.ctrlr.background.encryptionCache = {}; var tot = 0; for (var i = 0; i < query.length; i++){ var panel=query[i]; for (var j = 0; j < panel.length; j++){ if (panel[j].sensitive) { i2b2.MedCo.ctrlr.background.toBeEncrypted(panel[j].values) tot += panel[j].values.length } } } document.getElementById("MedCoTest-EncryptTot").innerHTML = tot; document.getElementById("MedCoTest-EncryptCurr").innerHTML = 0; // start timer var dothis = function(){ document.getElementById("MedCoTest-EncryptCurr").innerHTML = tot - i2b2.MedCo.ctrlr.background.remainingToEncrypt; }; var done = function(){ if (i2b2.MedCo.ctrlr.background.encryptionDone()){ i2b2.MedCo.test.ctrlr.encrypted = true; return true } return false }; this.startTimer(startTime, "MedCoTest-EncryptTime", done, dothis); }, send: function(){ if (this.doing){ alert("Already doing something.") return } // check the query has been encrypted if (!this.encrypted){ alert("First encrypt the query.") return } this.doing = true; var startTime = new Date().getTime(); // get query var query = this.getQuery(); // clear panels and put in their model the parameters i2b2.MedCo.QT.ctrlr.clear(); for (var i = 0; i < query.length; i++){ var panel=query[i]; for (var j = 0; j < panel.length; j++){ i2b2.MedCo.QT.panels[i].model.content.push(panel[j]) } } var numQueries = this.getNumQueries(); var remaining = numQueries; var queryTimes = []; function sendQuery() { var startTime = new Date().getTime(); this.MedCoparams = {}; this.MedCoparams.psm_query_definition = i2b2.MedCo.QT.query.buildQueryDefinition("MedCo_query"); this.MedCoparams.psm_result_output = "\n\n"; // callback processor to run the query from definition this.MedCocallback = new i2b2_scopedCallback(); this.MedCocallback.scope = this; this.MedCocallback.callback = function (results) { var endTime = new Date().getTime(); queryTimes.push(endTime-startTime); remaining -= 1; // extract the server times try{ if (results.error) { alert(results.errorMsg); return; } else { i2b2.MedCo.test.ctrlr.response = results; } } catch(e){ alert("Error when extracting the results of the query: " + e.message) } if (remaining > 0){ // other queries to be sent sendQuery(); } }; i2b2.CRC.ajax.runQueryInstance_fromQueryDefinition("PLUGIN:MedCo", this.MedCoparams, this.MedCocallback); } sendQuery(); document.getElementById("MedCoTest-QueryTimeMean").innerHTML = "-"; document.getElementById("MedCoTest-QueryTimeVariance").innerHTML = "-"; // show tot response count document.getElementById("MedCoTest-QueryTot").innerHTML = numQueries; // start timer var dothis = function(){ document.getElementById("MedCoTest-QueryCurr").innerHTML = numQueries - remaining; }; var done = function(){ if (remaining<=0){ // done sending queries. clear panels i2b2.MedCo.QT.ctrlr.clear(); // compute mean time var mean = 0; - for (i=0; i stop the timer) // dothis: if given this function is while updating the timer this.clearTimer(); this.startTime = startTime; this.timeinterval = setInterval(function(){i2b2.MedCo.test.ctrlr.updateTimer(label, stop, dothis)}, 100); }, updateTimer: function(label, stop, dothis){ if (dothis instanceof Function) { dothis(); } var now = new Date().getTime(); document.getElementById(label).innerHTML = prettyTime(now-this.startTime); if (stop()){ this.stopTimer() } }, clearTimer: function(){ this.startTime = null; clearInterval(this.timeinterval); this.timeinterval = null; }, stopTimer: function(){ this.clearTimer(); this.doing = false; } }; function prettyTime(milliseconds){ return (milliseconds/1000).toFixed(2) } \ No newline at end of file