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

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

Open

    sidPromise.then(function success(validSamples) {
      Sample.get(
        {'id__in': validSamples, 'limit': 0}, // parameters of GET
        function success(response) {
          // If no valid sample records are found, report the error.

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

Open

                function success(responseObject) {
                  // Function that calculates input gene's expression value
                  // based on the input array of base and comparison sums.
                  var calcGeneExpr = function(geneID, exprTracker) {
                    // Do nothing if the length of exprTracker is not 4, or one

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

Open

  function DownloadController($window, $log, AnnotationTypes) {
    var self = this;
    self.queryStatus = 'Connecting to the server ...';
    self.fixedTypes = ['experiment', 'sample_name', 'ml_data_source'];
    self.includedTypes = [];

Function getSignatureSetPromise has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    getSignatureSetPromise: function(pkArr) {
      // Check for any pk already cached, then retrieve what's missing in
      // bulk via the set endpoint on the signature API. Return a promise and
      // supply a callback that populates the cache when the API returns.
      var cbSampleBin = this; // closure link to SampleBin for callbacks

Function create_participations has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

    def create_participations(num_signatures, num_genes):
        """
        Static method that builds Participation table based on the input
        number of signatures and number of genes.
        """

• Read up
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Function controller has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        function($scope, UserFactory, $uibModal, $rootScope, $window) {
          UserFactory.getPromise().then(function() {
            $scope.userObj = UserFactory.getUser();
          });

Function setUp has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def setUp(self):
        super(APIResourceTestCase, self).setUp()
        # create a test experiment to retrive with the API
        self.test_experiment = ModelsTestCase.experiment_data
        ModelsTestCase.create_test_experiment(

Function updateHeatmapActivity has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var updateHeatmapActivity = function() {
          // when all promises are fulfilled, we can update vegaData
          var newActivity = [];
          var excludeSamples = [];

Function SignatureController has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function SignatureController($stateParams, Signature, $log, errGen) {
    var self = this;
    self.isValidModel = false;
    // Do nothing if the model ID in URL is falsey. The error will be taken
    // care of by "<ml-model-validator>" component.

Function show has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

Function getSampleListPromise has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    Sample.getSampleListPromise = function(pkList) {
      return $q(function(resolve, reject) {
        var cachedSamples = [];
        var promisedSampleIDs = [];
        var newSamplePromises = [];

Function searchGenes has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        $scope.searchGenes = function(val) {
          $scope.loadingGenes = true;
          var qparams = {
            'query': val,
            'organism': $scope.organism

Function controller has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    controller: ['$scope', 'Gene', function($scope, Gene) {
      $scope.errors = null;

      $scope.searchGenes = function() {
        // Gene.search will query for all of the search terms in qparams,

Function openLoginModal has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

          $scope.openLoginModal = function() {
            var modalInstance = $uibModal.open({
              templateUrl: 'tribe_client/tribe-login-modal.tpl.html',
              controller: [
                '$scope', '$uibModalInstance', 'TribeSettings',

Function get has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      get: function() {
        $scope.results = [];
        $scope.search.query.status = '';
        if (!$scope.search.query.text) {
          $log.info('Query text is empty, so skipping search.');

Function SignatureController has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function SignatureController(Signature, $stateParams, MlModelTracker, $log,
                               errGen) {
    var self = this;
    if (!$stateParams.id) {
      self.statusMessage = 'Please specify signature ID in the URL.';

Function getSampleIDPromise has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    var getSampleIDPromise = function() {
      var deferred = $q.defer();
      // If 'signature' is found in the URL, get the activity values based on
      // signature and sample(s):
      if ($stateParams.signature) {

Function getEnrichedSignatures has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    var getEnrichedSignatures = function() {
      participations.forEach(function(element) {
        var sigID = element.signature;
        if (!self.signatures[sigID]) {
          return;