Function exports has 471 lines of code (exceeds 25 allowed). Consider refactoring.

Open

module.exports = function ( grunt ) {

  /**
   * Load required Grunt tasks. These are installed based on the versions listed
   * in `package.json` when you do `npm install` in this directory.

File tests.py has 945 lines of code (exceeds 250 allowed). Consider refactoring.

Open

# coding: utf-8 (see https://www.python.org/dev/peps/pep-0263/)

from __future__ import unicode_literals
from __future__ import print_function
import os

Function GeneNetworkController has a Cognitive Complexity of 103 (exceeds 5 allowed). Consider refactoring.

Open

    function GeneNetworkController(
      $stateParams, Edge, Signature, Gene, ExpressionValue, $log, errGen,
      $httpParamSerializerJQLike, $scope, MlModelTracker, $timeout
    ) {
      var self = this;

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Function GeneNetworkController has 414 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function GeneNetworkController(
      $stateParams, Edge, Signature, Gene, ExpressionValue, $log, errGen,
      $httpParamSerializerJQLike, $scope, MlModelTracker, $timeout
    ) {
      var self = this;

File network.js has 477 lines of code (exceeds 250 allowed). Consider refactoring.

Open

/**
 * "adage.gene.network" module.
 */

angular.module('adage.gene.network', [

File Gruntfile.js has 473 lines of code (exceeds 250 allowed). Consider refactoring.

Open

module.exports = function ( grunt ) {

  /**
   * Load required Grunt tasks. These are installed based on the versions listed
   * in `package.json` when you do `npm install` in this directory.

Function bootstrap_database has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.

Open

def bootstrap_database(annotation_fh, dir_name=None):
    """
    Import initial experiment, sample and annotation data to initialize the
    ADAGE database. Assumes we are starting with an empty database, so this
    will fail if any existing data are found that conflict with what is being

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APIResourceTestCase has 45 functions (exceeds 20 allowed). Consider refactoring.

Open

class APIResourceTestCase(ResourceTestCaseMixin, TestCase):
    # API tests:
    # For most of our interfaces, we should be able to GET, but every other
    # REST API should fail: POST, PUT, PATCH, DELETE. There are a few
    # exceptions for which we allow POST but the behavior is the same as GET.

Function EnrichedSignatureController has 149 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

File api.py has 414 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from django.conf.urls import url
from django.core.exceptions import ObjectDoesNotExist
from django.db.models import Q
from django.http import HttpResponse
from organisms.api import OrganismResource

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

Open

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

angular.module('adage.signature', [

Function check_and_import has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.

Open

def check_and_import(file_handle, ml_model):
    """Read valid data lines into the database.  An exception will be raised
    if any errors are detected in file_handle.
    """
    # If the database already includes record(s) of the same ml_model,

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Function drawNetwork has 103 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      function drawNetwork() {
        // Calculate svg size.
        var minSvgSize = 600;  // Minimum size of svg.
        var maxSvgSize = 1280; // Maximum size of svg.
        var svgSize = genes.length * 10;

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

Open

        function success(responseObject) {
          var edgeList = responseObject.objects;
          // Collect a list of distinct genes for query.
          var geneList = getQueriedGenes(edgeList);
          // Now retrieve the Gene objects using the geneList.

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 success has 74 lines of code (exceeds 25 allowed). Consider refactoring.

Open

            function success(responseObject) {
              setGenes(responseObject);
              if (genes.length === 0) {
                self.statusMessage =
                  'Gene(s) not found, please check the gene ID.';

Function getVolcanoPlotData has 68 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    getVolcanoPlotData: function() {
      // use sample lists for base-group and comp-group to produce output for
      // the volcano plot of the form:
      //   signature - diff - logsig,
      // where:

Function check_and_import has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

def check_and_import(file_handle, ml_model, participation_type):
    """Read valid data lines into the database.  An exception will be
    raised if any errors are detected in file_handle.
    """
    signatures_in_file = set()

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Function rebuildHeatmapActivity has 64 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      rebuildHeatmapActivity: function() {
        if (!this.mlmodel.id) {
          // ignore "rebuild" requests until a model is specified
          $log.info(
            'rebuildHeatmapActivity: skipping because mlmodel=', this.mlmodel