cBioPortal/iViz

Function getSampleClinicalData has 61 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

Function ready has 61 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    ready: function() {
      var _self = this;
      var callbacks = {};
      var attrId = this.attributes.attr_id;

Function getTickFormat has 61 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    content.getTickFormat = function(v, logScale, data_, opts_) {
      var _returnValue = v;
      var index = 0;
      var e = d3.format('.1e');// convert small data to scientific notation format
      var formattedValue = '';

Function initDCPieChart has 60 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function initDCPieChart() {
      if (v.opts.hasOwnProperty('chartId') &&
        v.data.hasOwnProperty('ndx') &&
        v.data.hasOwnProperty('attr_id')) {
        var width = v.opts.width || 130;

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

Open

      _.each(_allSamples, function(samples, studyId) {
        _.each(samples, function(sampleId) {
          tableData_.cna_details.allSamples.push({
            "molecularProfileId": window.iviz.datamanager.getCNAProfileIdByStudyId(studyId),
            "sampleId": sampleId

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

Open

      _.each(_allSamples, function(samples, studyId) {
        _.each(samples, function(sampleId) {
          tableData_.mutated_genes.allSamples.push({
            "molecularProfileId": window.iviz.datamanager.getMutationProfileIdByStudyId(studyId),
            "sampleId": sampleId

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Function setSelectedCases has 58 lines of code (exceeds 25 allowed). Consider refactoring.

Open

            setSelectedCases: function(selectionType, selectedCases) {
              var radioVal = selectionType;
              var selectedCaseUIDs = [];
              var unmappedCaseIDs = [];

Function SurvivalChartProxy has 58 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  iViz.data.SurvivalChartProxy = function(_data, _attrId) {
    var datumArr_ = [];

    // convert raw data
    var _totalNum = 0;

Function getConfigs has 58 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        function(self, fetch_promise) {
          if (_.isObject(configs_)) {
            fetch_promise.resolve(configs_);
          } else {
            $.getJSON(window.cbioResourceURL + 'configs.json?' + window.appVersion)

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

Open

    template: '<div class="chart-header" id="{{chartId}}-chart-header">' +
    '<div class="chart-title" ' +
    ':class="[showOperations?chartTitleActive:chartTitle]" ' +
    'v-if="hasChartTitle">' +
    '<span class="chart-title-span" id="{{chartId}}-title">{{displayName}}' +

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

Open

    template: '<div id={{chartDivId}} ' +
    'class="grid-item grid-item-w-2 grid-item-h-1 bar-chart" ' +
    ':attribute-id="attributes.attr_id" @mouseenter="mouseEnter" ' +
    ':layout-number="attributes.layout" ' +
    '@mouseleave="mouseLeave">' +

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

Open

        if (this.showPieIcon) {
          this.$nextTick(function() {
            $('#' + this.chartId + '-chart-header .fa-pie-chart').qtip($.extend(true, this.titleIconQtipOpts, {
              content: {
                text: 'Convert table to pie chart'

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

Open

        if (this.showTableIcon) {
          this.$nextTick(function() {
            $('#' + this.chartId + '-chart-header .fa-table').qtip($.extend(true, this.titleIconQtipOpts, {
              content: {
                text: 'Convert pie chart to table'

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

Open

        _.each(categories, function(category) {
          if (dataForCategories.hasOwnProperty(category.name)) {
            groups.push({
              name: category.name,
              caseIds: dataForCategories[category.name],

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

Open

        _.each(categories, function(category) {
          if (dataForCategories.hasOwnProperty(category.name)) {
            groups.push({
              name: category.name,
              caseIds: dataForCategories[category.name],

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Function getColors has 55 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    content.getColors = function() {
      return [
        '#2986e2', '#dc3912', '#f88508', '#109618',
        '#990099', '#0099c6', '#dd4477', '#66aa00',
        '#b82e2e', '#316395', '#994499', '#22aa99',

Function downloadCaseData has 53 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    downloadCaseData: function() {
      var _def = new $.Deferred();
      var sampleUIds_ = vm_.selectedsampleUIDs;
      var attr = {};
      var self = this;

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

Open

            $('#' + chartId + '-pdf', api.elements.tooltip).click(function() {
              iViz.util.download(self.chartCtrl.getChartType(), 'pdf', self.chartCtrl.getDownloadData('pdf'));
            });

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

Open

            $('#' + chartId + '-svg', api.elements.tooltip).click(function() {
              iViz.util.download(self.chartCtrl.getChartType(), 'svg', self.chartCtrl.getDownloadData('svg'));
            });

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

Open

                if (!_.isArray(_metaObj.priority)) {
                  iViz.priorityManager
                    .setClinicalAttrPriority(_metaObj.attr_id, Number(_metaObj.priority));
                  _metaObj.priority =
                    iViz.priorityManager

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