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"];

// Query A:
//  -panel 1:
//      cutaneous_melanoma
//  -panel 2:
//      braf_gene
//  -panel 3:
//      protein_600
var queryA = [
    [cutaneous_melanoma],
    [braf_gene],
    [protein_600]
];

// Query B:
// -panel 1:
//      cutaneous_melanoma
// -panel 2:
//      braf_gene
// -panel 3:
//      pten_gene, cdkn2a_gene, map2k1_gene, mpa2k2
var queryB = [
    [cutaneous_melanoma],
    [braf_gene],
    [pten_gene, cdkn2a_gene, map2k1_gene, mpa2k2]
];

i2b2.MedCo.test.ctrlr = {
    // time the action started
    startTime: null,

    // whether the query has been encrypted
    encrypted: false,

    encrypting: false,

    // pointer to the interval object so to stop it
    timeinterval: null,

    encrypt: function(){
        if (this.doing){
            alert("Already doing something.")
            return
        }
        this.doing = true;

        // start timer
        var dothis = function(){
            document.getElementById("MedCo-EncryptCurr").innerHTML = i2b2.MedCo.ctrlr.background.remaining;
        };

        this.startTimer("MedCo-EncryptTime", i2b2.MedCo.ctrlr.background.done, dothis);

        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++){
                i2b2.MedCo.ctrlr.background.toBeEncrypted(panel[j])
                tot += panel[j].length
            }
        }
        document.getElementById("MedCo-EncryptTot").innerHTML = tot;
    },

    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 query = this.getQuery();

        // callback processor to run the query from definition
        this.MedCocallback = new i2b2_scopedCallback();
        this.MedCocallback.scope = this;
        this.MedCocallback.callback = function(results) {
            // //		"results" object contains the following attributes:
            // //			refXML: xmlDomObject <--- for data processing
            // //			msgRequest: xml (string)
            // //			msgResponse: xml (string)
            // //			error: boolean
            // //			errorStatus: string [only with error=true]
            // //			errorMsg: string [only with error=true]

            // stop the timer and the gif
            i2b2.MedCo.QT.timer.stop();

            try{
                if (results.error) {
                    alert(results.errorMsg);
                    return;
                } else {
                    // extract and show the patient counts
                    i2b2.MedCo.QT.query.showResponse(results);
                }
            } catch(e){
                alert("Error when extracting the results of the query: " + e.message)
            }
        };

        this.MedCoparams = {};
        this.MedCoparams.psm_query_definition = i2b2.MedCo.QT.query.buildQueryDefinition("MedCo_query");
        this.MedCoparams.psm_result_output = "<result_output_list><result_output priority_index=\"9\" name=\"patient_count_xml\"/>\n</result_output_list>\n";

        i2b2.CRC.ajax.runQueryInstance_fromQueryDefinition("PLUGIN:MedCo", this.MedCoparams, this.MedCocallback);

    },

    getQuery: function(){
        var query = null;
        switch(document.getElementById('MedCo-QueryType').value) {
            case "A":
                query = queryA;
                break;
            case "B":
                query = queryB;
                break;
            default:
                alert("Query type not recognized.")
                return
        }

        return query
    },

    getNumQueries: function(){
        return parseInt(document.getElementById('MedCo-NumQueries').value)
    },

    queryChanged: function(){
        this.encrypted = false;
    },

    startTimer: function(label, stop, dothis){
        // label: id of the html object in which write the time
        // stop: function which returns a boolean (true if the action has been completed => stop the timer)
        // dothis: if given this function is while updating the timer
        this.stopTimer();
        this.startTime = new Date().getTime();
        this.timeinterval = setInterval(function(){i2b2.MedCo.test.ctrlr.updateTimer(label, stop, dothis)}, 100);
    },

    updateTimer: function(label, stop, dothis){
        dothis();
        var now = new Date().getTime();
        document.getElementById(label).innerHTML = ((now-this.startTime)/1000).toFixed(2);
        if (stop()){
            this.stopTimer()
        }
    },

    stopTimer: function(){
        clearInterval(this.timeinterval);
        this.timeinterval = null;
        this.doing = false;
    }
};