cBioPortal/iViz

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

Open

          if (smallerOutlier.length > 0) {
            this.data.min = Number(_.max(smallerOutlier));
            this.data.smallerOutlier = this.data.min;
          }

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

Open

        animateTable('#' + v.opts.chartDivId, 'pie', function() {
          vm.$dispatch('update-grid');
          $('#' + v.opts.chartDivId).css('z-index', '1');
        });

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

Open

          if (greaterOutlier.length > 0) {
            this.data.max = Number(_.min(greaterOutlier));
            this.data.greaterOutlier = this.data.max;
          }

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

Open

        animateTable('#' + v.opts.chartDivId, 'table', function() {
          vm.$dispatch('update-grid');
          $('#' + v.opts.chartDivId).css('z-index', '');
        });

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Identical blocks of code found in 3 locations. Consider refactoring.

Open

        this.$dispatch('create-rainbow-survival', {
          attrId: this.attributes.attr_id,
          subtitle: ' (' + this.attributes.display_name + ')',
          groups: groups,
          groupType: this.attributes.group_type

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Identical blocks of code found in 3 locations. Consider refactoring.

Open

        this.$dispatch('create-rainbow-survival', {
          attrId: this.attributes.attr_id,
          subtitle: ' (' + this.attributes.display_name + ')',
          groups: groups,
          groupType: this.attributes.group_type

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

Open

  iViz.view.component.SurvivalCurve.prototype.removeNoInfo = function() {
    var _self = this;
    _self.elem_.svg.selectAll('.noInfo').remove();
  };

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Function update-filters has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      'update-filters': function(redrawGroup) {
        if (!this.clearGroup) {
          if (redrawGroup) {
            dc.redrawAll(this.id);
          }

Function generateVSDescription_ has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    var generateVSDescription_ = function(_studies, _filters) {
      var _desp = '';
      if (_studies.studies.length > 0) {
        _desp = _studies.count + (_studies.count > 1 ? ' samples ' : ' sample ')
          + 'from ' + _studies.studies.length +

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

Open

    content.updateDataForDownload = function(fileType) {
      if (fileType === 'tsv') {
        initTsvDownloadData();
      } else if (['pdf', 'svg'].indexOf(fileType) !== -1) {
        initCanvasDownloadData();

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Similar blocks of code found in 3 locations. Consider refactoring.

Open

      var labelMaxFreq = _.last(_.sortBy(_.pluck(labels, 'sampleRate'),
        function(item) {
          return item.toString().length;
        })).toString().length;

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Similar blocks of code found in 3 locations. Consider refactoring.

Open

      var labelMaxName = _.last(_.sortBy(_.pluck(labels, 'name'),
        function(item) {
          return item.toString().length;
        })).toString().length;

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

Open

    content.updateDataForDownload = function(fileType) {
      if (fileType === 'tsv') {
        initTsvDownloadData();
      } else if (['pdf', 'svg'].indexOf(fileType) !== -1) {
        initCanvasDownloadData();

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Similar blocks of code found in 3 locations. Consider refactoring.

Open

      var labelMaxNumber = _.last(_.sortBy(_.pluck(labels, 'cases'),
        function(item) {
          return item.toString().length;
        })).toString().length;

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Function getClinicalAttributesByStudy has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        function(self, fetch_promise) {
          $.get(window.cbioURL + 'api/clinical-attributes?projection=SUMMARY&pageSize=100000&pageNumber=0&direction=ASC')
            .done(function(data) {
              var attributes = {};
              _.each(data, function(attribute) {

Function initTsvDownloadData has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function initTsvDownloadData() {
      var attrs =
        iViz.util.tableView.getAttributes(type_).filter(function(attr) {
          return attr.attr_id !== 'uniqueId' && (_.isBoolean(attr.show) ? attr.show : true);
        });

Function ready has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    ready: function() {
      var _self = this;
      var attrId =
        this.attributes.group_type === 'patient' ? 'patient_uid' : 'sample_uid';
      this.invisibleDimension = this.ndx.dimension(function(d) {

Function getCnaFractionData has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        function(self, fetch_promise) {
          var _ajaxCnaFractionData = {};
          var cancer_study_ids = self.getCancerStudyIds();
          var _studyCasesMap = self.getStudyCasesMap();
          var fetch_promises = [];

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

Open

        $.ajax({
          type: 'POST',
          url: window.cbioURL + 'api/gene-panel-data/fetch',
          data: JSON.stringify({
            "sampleMolecularIdentifiers": map

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

Open

            $.ajax({
              type: 'POST',
              url: window.cbioURL + 'api/samples/fetch?projection=SUMMARY',
              data: JSON.stringify({
                "sampleIdentifiers": data

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