greenelab/adage-server

File signature.js has 375 lines of code (exceeds 250 allowed). Consider refactoring.

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/**
 * "adage.signature" module.
 */

angular.module('adage.signature', [

Function link has 90 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      link: function($scope) {
        $scope.queryStatus = 'Connecting to the server ...';
        $scope.activities = {};
        $scope.experiments = [];
        $scope.topMode = true;

Function link has 88 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 50 lines of code (exceeds 25 allowed). Consider refactoring.

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

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

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

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

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

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.';

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

Open

        $scope.setMode = function() {
          $scope.topMode = !$scope.topMode;
          $scope.numGenesetsShown =
            $scope.topMode ? $scope.topNum : $scope.enrichedGenesets.length;
        };

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

Open

        $scope.setMode = function() {
          $scope.topMode = !$scope.topMode;
          $scope.numGenesShown =
            $scope.topMode ? $scope.topNum : $scope.genes.length;
        };

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