File models_controller.rb has 452 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'libxml'
require 'bives'

class ModelsController < ApplicationController

File assays.js has 450 lines of code (exceeds 250 allowed). Consider refactoring.

Open

var sops_assets=new Array();
var models_assets=new Array();
var data_files_assets=new Array();
var organisms = new Array();
var assays_array = new Array();

File application_controller.rb has 449 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'authenticated_system'

class ApplicationController < ActionController::Base

  include Seek::Errors::ControllerErrorHandling

Method dictionary_definition has 164 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def dictionary_definition
      # in the future this could be moved out to a file
      { refresh: 'famfamfam_silk/arrow_refresh_small.png',
        arrow_up: 'famfamfam_silk/arrow_up.png',
        arrow_down: 'famfamfam_silk/arrow_down.png',

Function Position has a Cognitive Complexity of 42 (exceeds 5 allowed). Consider refactoring.

Open

function Position(x, y)
{
  this.X = x;
  this.Y = y;
  

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Function Position has a Cognitive Complexity of 42 (exceeds 5 allowed). Consider refactoring.

Open

function Position(x, y)
{
  this.X = x;
  this.Y = y;
  

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Method extended_xml has a Cognitive Complexity of 42 (exceeds 5 allowed). Consider refactoring.

Open

  def extended_xml builder,object        
    
    submitter = determine_submitter object
    builder.tag! "submitter" do 
      api_partial(builder,submitter)

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Method log_event has a Cognitive Complexity of 42 (exceeds 5 allowed). Consider refactoring.

Open

  def log_event
    User.with_current_user current_user do
      c = self.controller_name.downcase
      a = self.action_name.downcase

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Function prototype has 160 lines of code (exceeds 25 allowed). Consider refactoring.

Open

Searcher.prototype = new function() {
  // search is performed in chunks of 1000 for non-blocking user input
  var CHUNK_SIZE = 1000;
  // do not try to find more than 100 results
  var MAX_RESULTS = 100;

Method tree_editor_display has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring.

Open

  def tree_editor_display type, show_edit=true, show_delete=true, selected_id=nil, related_resource_type="Person",selective_display=false, foldable=false

    selected_display_items = nil

    if selected_id && selective_display

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File policy.rb has 400 lines of code (exceeds 250 allowed). Consider refactoring.

Open

class Policy < ActiveRecord::Base
  
  has_many :permissions,
           :dependent => :destroy,
           :order => "created_at ASC",

Function ResizeableTextbox has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.

Open

function ResizeableTextbox(id, parent)
{
  var MINWIDTH = 125;
  var MINHEIGHT = 80;
  var MINSIZE = 38;

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Method create has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.

Open

  def create
    if handle_upload_data

      @data_file = DataFile.new params[:data_file]

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Method indented_child_options has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.

Open

        def indented_child_options type, parent, depth=0, selected_id

          result = []
          unless parent.children.empty?
            parent.children.sort { |a, b| a.title.downcase <=> b.title.downcase }.each do |child|

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File admins_controller.rb has 399 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'delayed/command'

class AdminsController < ApplicationController
  include CommonSweepers

Class User has 41 methods (exceeds 20 allowed). Consider refactoring.

Open

class User < ActiveRecord::Base
  acts_as_annotation_source
  include SavageBeast::UserInit

  acts_as_tagger

Function ResizeableContainer has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring.

Open

function ResizeableContainer(contentID, parent)
{
  var MINSIZE = 38;
  var EDGE_THICKNESS = 7;
  var EDGEDIFFSIZE = 2*EDGE_THICKNESS + 3;

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Method append_list_assay_organisms has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring.

Open

  def append_list_assay_organisms assay_organisms
    result=""

    organism=nil
    strain = nil

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Method set_attributes_with_sharing has a Cognitive Complexity of 35 (exceeds 5 allowed). Consider refactoring.

Open

  def set_attributes_with_sharing sharing, projects
    # if no data about sharing is given, it should be some user (not the owner!)
    # who is editing the asset - no need to do anything with policy / permissions: return success
    self.tap do |policy|
      if sharing

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Method get_resource_hash has a Cognitive Complexity of 35 (exceeds 5 allowed). Consider refactoring.

Open

  def get_resource_hash scale, external_resource_hash
    internal_resource_hash = {}
    if external_resource_hash.blank?
      @results_scaled[scale].each do |item|
        tab = item.respond_to?(:tab) ? item.tab : item.class.name

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