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

Open

angular.module('adage.participation.resources', [
  'ngResource',
  'adage.utils'
])

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

Open

angular.module('adage.signature.resources', [
  'ngResource',
  'adage.utils'
])

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

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

      self.search = {};

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

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    findEnrichedSignatures: function(scope, state) {
      var geneIds = Object.keys(scope.selectedGenes);
      var geneString = geneIds.join();

      state.go('enriched_signatures', {

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

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

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

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    sendToNetwork: function(scope, state) {
      var geneIds = Object.keys(scope.selectedGenes);
      var geneString = geneIds.join();

      state.go('gene_network', {

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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 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 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 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 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 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 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 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);

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

Open

      function($scope, SelectedGenesFactory, CommonGeneFuncts) {
        $scope.buttonPage = 1;
        $scope.queryResults = $scope.searchResults[$scope.query];

        var selectedGenes = SelectedGenesFactory.returnGenes();

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

Open

      ctrl.show = function(id) {
        if (!id) {
          $log.warn(
            'adage.experimentDetail.component: show() called with id',
            id