Function controller has 56 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function(Experiment, Sample, $log) {
      var ctrl = this;

      ctrl.$onInit = function() {
        ctrl.experiment = {

Function build_search_kwargs has 17 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def build_search_kwargs(self,

Function controller has 51 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function($log, Heatmap, HeatmapSpec, Sample) {
      var ctrl = this;

      // objects needed for Vega
      ctrl.heatmapSpec = HeatmapSpec;

Function calculateEnrichments has 50 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var calculateEnrichments = function(geneGenesets, allGenesetInfo,
                                            totalGeneNum, cutoff) {
          var N = totalGeneNum;

          // This will be the number of genes from the high weight gene list

Function controller has 48 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function(Sample, Experiment, $log) {
      var ctrl = this;
      ctrl.makeHref = Experiment.makeHref;

      ctrl.$onInit = function() {

Function EnrichedSignatureController has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  function EnrichedSignatureController($stateParams, Signature, Participation,
    Gene, MlModelTracker, MathFuncts, pValueCutoff, pValueDigits, $scope, $q,
    $log, errGen) {
    var self = this;
    self.isValidModel = false;

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Function AnalysisCtrl has 45 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function AnalysisCtrl($scope, $log, $q, $state, $stateParams,
  SampleBin, Sample) {
  $scope.isValidModel = false;
  // Do nothing if mlmodel in URL is falsey. The error will be taken
  // care of by "<ml-model-validator>" component.

Function calculateEnrichments has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    var calculateEnrichments = function(typeName, genesBySignatures) {
      var m = genesInUrl.length,
        N = self.geneNum,
        pValueArray = [],
        matchedGenesBySignature = [],

Function controller has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      function($scope, $state, Gene, SelectedGenesFactory, CommonGeneFuncts) {
        var numResultsToReturn = 10;
        $scope.errors = null;
        $scope.autocompleteQuery = '';
        $scope.selectedGenes = SelectedGenesFactory.returnGenes();

Function link has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      link: function($scope) {
        $scope.queryStatus = 'Connecting to the server ...';

        $scope.topMode = true;
        $scope.topNum = 3;

Function controller has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function($log, Genesets, Gene, errGen) {
      var self = this;

      self.search = {};

Function SearchCtrl has 40 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function SearchCtrl($scope, $log, $location, Search) {
    $scope.results = [];
    $scope.search = {
      query: {
        text: '',

Function get_annotations has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def get_annotations(request=None, **kwargs):
        """
        Return a tab-delimited file containing all samples for every Experiment
        with Sample properties for each and all annotations (by default) or, if
        `annotation_types` is specified, return only those annotation types for

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Function controller has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      function($scope, SelectedGenesFactory) {
        $scope.currentPage = 1;
        $scope.itemsPerPage = 10;
        $scope.totalResults = 0;
        $scope.maxSize = 10;

Function mapSignaturesToSignatureInfo has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      var mapSignaturesToSignatureInfo = function() {
        // (2a) next, we build an array (replacing `volcanoData.source`)
        //      comprised of `signatureObject`s by walking through the
        //      `firstSampleSignatures` and constructing a `signatureObject` for
        //      each. [outer .map()]

Function handleExperimentResponse has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var handleExperimentResponse = function(response) {
          // enhanceExpData: a function that enhances the given experiment.
          // The enhancements include:
          // (1) Convert entries in sample_set from sample URI to sample ID,
          //     and delete samples that are not related to current signature;

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

Open

      self.searchGenesets = function() {
        self.searchStatus = 'Searching for gene sets...';
        var qparams = {
          'query': self.search.query,
          'organism__scientific_name': self.organism,

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

Open

  function VolcanoPlotViewCtrl(SampleBin, $stateParams) {
    var ctrl = this;
    ctrl.isValidModel = false;
    // Do nothing if mlmodel in URL is falsey. The error will be taken
    // care of by "<ml-model-validator>" component.

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

Open

  this.setSpec = function(activities) {
    var activityArr = [];
    var samples = Object.keys(activities);
    samples.forEach(function(sampleID, index) {
      activityArr.push({

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

Open

        function showEdgeTip(data) {
          geneTip.hide(); // Hide gene-tip window (if any) first.
          var weightPrecision = 3;
          var htmlText = 'Edge weight: ';
          htmlText += data.weight.toFixed(weightPrecision);