cBioPortal/iViz

'use strict';
/**
 * Data proxy for survival chart.
 *
 * @param {array} _data Data
 * @param {string} _attrId Chart type: DFS_SURVIVAL or OS_SURVIVAL
 * @return {object} APIs
 */
(function(iViz, kmEstimator, _) {
  iViz.data.SurvivalChartProxy = function(_data, _attrId) {
    var datumArr_ = [];

    // convert raw data
    var _totalNum = 0;
    _.each(_data, function(_dataObj) {
      var _status;
      var _time;
      if (_attrId === 'DFS_SURVIVAL') {
        _time = _dataObj.DFS_MONTHS;
        _status = _dataObj.DFS_STATUS;
      } else if (_attrId === 'OS_SURVIVAL') {
        _time = _dataObj.OS_MONTHS;
        _status = _dataObj.OS_STATUS;
      }
      if (!isNaN(_time) &&
        _status !== 'NaN' && _status !== 'NA' &&
        typeof _status !== 'undefined' && typeof _time !== 'undefined') {
        var _datum = {
          study_id: '',
          patient_id: '',
          patient_uid: '',
          time: '', // num of months
          status: '',
          num_at_risk: -1,
          survival_rate: 0
        };
        _datum.patient_uid = _dataObj.patient_uid;
        _datum.patient_id = iViz.getCaseIdUsingUID('patient', _dataObj.patient_uid);
        _datum.study_id = _dataObj.study_id;
        _datum.time = parseFloat(_time);
        _datum.status = _status;
        datumArr_.push(_datum);
        _totalNum += 1;
      }
    });

    // convert status from string to number
    // os: DECEASED-->1, LIVING-->0; dfs: Recurred
    // Progressed --> 1, Disease Free-->0
    _.each(datumArr_, function(_datumObj) {
      var _status = _datumObj.status.toString().toLowerCase();
      if (_status === 'deceased' || _status === 'recurred/progressed' ||
        _status === 'recurred' || _status === 1) {
        _datumObj.status = 1;
      } else if (_status === 'living' || _status === 'disease free' ||
        _status === 'diseasefree' || _status === 'alive' || _status === 0) {
        _datumObj.status = 0;
      } else {
        // TODO : by default set status 0 when _status doesn't
        // match to any of the above cases, not sure whether to treat them as
        // living or not
        _datumObj.status = 0;
      }
    });

    // calculate num at risk
    datumArr_ = _.sortBy(datumArr_, 'time');
    for (var i in datumArr_) {
      if (datumArr_.hasOwnProperty(i)) {
        datumArr_[i].num_at_risk = _totalNum;
        _totalNum += -1;
      }
    }

    // calculate survival rate
    kmEstimator.calc(datumArr_);

    return {
      get: function() {
        return datumArr_;
      }
    };
  };
})(
  window.iViz,
  window.kmEstimator,
  window._
);