cBioPortal/iViz

Function mutatedGenesData has 71 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function mutatedGenesData(_selectedGenesMap, _selectedSampleUids) {
      genePanelMap = window.iviz.datamanager.updateGenePanelMap(genePanelMap, _selectedSampleUids);

      selectedGeneData.length = 0;
      var numOfCases_ = content.getCases().length;

Function Survival has 69 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  iViz.view.component.Survival = function() {
    var content_ = this;
    var opts_ = {
      downloadIsEnabled: true
    };

Function init has 68 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    content.init = function(_data, opts) {
      opts_ = $.extend(true, {}, opts);
      chartId_ = opts_.chartId;
      data_ = _.filter(_data, function(datum) {
        return !isNaN(datum.FRACTION_GENOME_ALTERED) && !isNaN(datum.MUTATION_COUNT);

Similar blocks of code found in 2 locations. Consider refactoring.

Open

      groups.push({
        type: 'patient',
        id: vm_.groupCount.toString(),
        selectedcases: [],
        hasfilters: false,

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

      groups.push({
        type: 'sample',
        id: vm_.groupCount.toString(),
        selectedcases: [],
        hasfilters: false,

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Function extractCnaData has 67 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    extractCnaData: function(_cnaData, _allSamples) {
      var _cnaMeta = {};
      var _allCNAGenes = {};
      var _cnaMetaIndex = 0;
      var self = this;

Function updateDataObject has 67 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    updateDataObject: function(type, attrIds) {
      var def = new $.Deferred();
      var self_ = this;
      var isPatientAttributes = (type === 'patient');
      var _data = isPatientAttributes ? data_.groups.patient.data : data_.groups.sample.data;

Similar blocks of code found in 2 locations. Consider refactoring.

Open

    function initCanvasDownloadData() {
      content.setDownloadData('svg', {
        title: opts_.title,
        chartDivId: opts_.chartId,
        fileName: opts_.title

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    function initCanvasDownloadData() {
      content_.setDownloadData('svg', {
        title: opts_.title,
        chartDivId: opts_.chartId,
        fileName: opts_.title

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Function barChartCanvasDownload has 66 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function barChartCanvasDownload(data, downloadOpts) {
      var _svgElement = '';
      var _svg = $('#' + data.chartId + '>svg').clone();
      var _svgWidth = Number(_svg.attr('width'));
      var _svgHeight = Number(_svg.attr('height')) + 20;

Function update has 66 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    content.update = function(_selectedSampleUIDs, _selectedRows) {
      var selectedMap_ = {};
      var includeMutationCount = false;
      if (_selectedRows !== undefined) {
        selectedRows = _selectedRows;

Function stat has 66 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    stat: function() {
      var _result = {};
      _result.origin = window.cohortIdsList;
      _result.filters = {};
      var self = this;

File barChartTemplate.js has 276 lines of code (exceeds 250 allowed). Consider refactoring.

Open

/**
 * Created by Karthik Kalletla on 4/6/16.
 */
'use strict';
(function(Vue, d3, dc, iViz, _, $, cbio) {

Function getPatientClinicalData has 65 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    var getPatientClinicalData = function(self, attr_ids) {
      var def = new $.Deferred();
      var fetch_promises = [];
      var clinical_data = {};
      if (_.isArray(attr_ids)) {

Identical blocks of code found in 2 locations. Consider refactoring.

Open

                if (_metaObj.datatype === 'NUMBER') {
                  _metaObj.view_type = 'bar_chart';
                  _metaObj.layout = [-1, 2, 'h'];
                } else if (_metaObj.datatype === 'STRING') {
                  _metaObj.view_type = 'pie_chart';

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Identical blocks of code found in 2 locations. Consider refactoring.

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                if (_metaObj.datatype === 'NUMBER') {
                  _metaObj.view_type = 'bar_chart';
                  _metaObj.layout = [-1, 2, 'h'];
                } else if (_metaObj.datatype === 'STRING') {
                  _metaObj.view_type = 'pie_chart';

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Function getLayoutMatrix has 63 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      getLayoutMatrix: function(layoutMatrix, chart) {
        var self_ = this;
        var neighborIndex;
        var foundSpace = false;
        var layout = chart.layout;

Identical blocks of code found in 2 locations. Consider refactoring.

Open

            if (typeof genePanelMap[item.gene] !== 'undefined') {
              freq = iViz.util.calcFreq(datum.cases, genePanelMap[item.gene].sampleNum);
            } else {
              freq = iViz.util.calcFreq(datum.cases, numOfCases_);
            }

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Identical blocks of code found in 2 locations. Consider refactoring.

Open

            if (typeof genePanelMap[item.gene] !== 'undefined') {
              freq = iViz.util.calcFreq(datum.cases, genePanelMap[item.gene].sampleNum);
            } else {
              freq = iViz.util.calcFreq(datum.cases, numOfCases_);
            }

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Function addChart has 62 lines of code (exceeds 25 allowed). Consider refactoring.

Open

            addChart: function(attrId) {
              var self_ = this;
              var attrData = self_.charts[attrId];
              var _attrAdded = false;
              var _group = {};