Method acts_as_asset has 67 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def acts_as_asset
        attr_accessor :parent_name
        include Seek::Taggable

        acts_as_scalable

Class Assay has 24 methods (exceeds 20 allowed). Consider refactoring.

Open

class Assay < ActiveRecord::Base

  include Seek::Rdf::RdfGeneration
  include Seek::OntologyTypeHandling
  include Seek::OntologyExtensionWithSuggestedType

Method get_stats has 66 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def get_stats
    collection = []
    type = nil
    title = nil
    @page=params[:id]

Method associate_tissue_and_cell_type has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

  def associate_tissue_and_cell_type tissue_and_cell_type_id,tissue_and_cell_type_title
       tissue_and_cell_type=nil
    if !tissue_and_cell_type_title.blank?
      if ( tissue_and_cell_type_id =="0" )
          found = TissueAndCellType.where(:title => tissue_and_cell_type_title).first

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Method update has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

  def update

    #FIXME: would be better to resolve the differences, rather than keep clearing and reading the assets and organisms
    #DOES resolve differences for assets now
    organisms             = params[:assay_organism_ids]||[]

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Method reset_password has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

  def reset_password
    user = User.find_by_reset_password_code(params[:reset_code] || "")

    respond_to do |format|
      if user

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Method administer_update has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

  def administer_update
    had_no_projects = @person.work_groups.empty?

    passed_params=    {:roles                 =>  User.admin_logged_in?,
                       :roles_mask            => User.admin_logged_in?,

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Method find_and_authorize_requested_item has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

  def find_and_authorize_requested_item
    begin
      name = self.controller_name.singularize
      action = translate_action(action_name)

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Method included has 62 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.included klass
        klass.class_eval do
          include ActsAsCachedTree
          after_update :touch_for_hierarchy_updates
          #add institution to ancestor projects

Function displayNormal has 61 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function displayNormal() {
    var xmlHttp;
    try {  // Firefox, Opera 8.0+, Safari  
        xmlHttp = new XMLHttpRequest(); 
        if (xmlHttp.overrideMimeType) {

Method new_or_update_mapping_links has 61 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def new_or_update_mapping_links compound, compound_annotation
    #create the mappings and mapping_links
     sabiork_id = compound_annotation["sabiork_id"]
     chebi_ids = compound_annotation["chebi_ids"]
     kegg_ids = compound_annotation["kegg_ids"]

File publications_controller.rb has 268 lines of code (exceeds 250 allowed). Consider refactoring.

Open

class PublicationsController < ApplicationController
  
  include IndexPager
  include DotGenerator
  include Seek::AssetsCommon

Method uniq_people_permissions_and_privileged_people has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

  def uniq_people_permissions_and_privileged_people(permissions, privileged_people)
    uniq_permissions_by_contributor permissions

    people_from_permissions = permissions.select{|p| p.contributor_type == 'Person'}.collect(&:contributor)

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Method initialize_default_folders has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

  def self.initialize_default_folders project, yaml_path=File.join(Rails.root,"config","default_data","default_project_folders.yml")
    raise Exception.new("This #{I18n.t('project')} already has folders defined") unless ProjectFolder.root_folders(project).empty?

    yaml = YAML.load(ERB.new(File.read(yaml_path)).result)
    folders={}

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Method create has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

  def create
    if handle_upload_data
      @presentation = Presentation.new(params[:presentation])

      @presentation.policy.set_attributes_with_sharing params[:sharing], @presentation.projects

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Method update has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

  def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:data_file]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:data_file].delete(column_name)

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Method update has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

  def update
    valid = true
    unless params[:author].blank?
      person_ids = params[:author].values.reject {|id_string| id_string == ""}
      if person_ids.uniq.size == person_ids.size

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Method paginate_after_fetch has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def paginate_after_fetch(collection, *args)
      options=args.pop unless args.nil?
      options ||= {}
      reorder = options[:reorder].nil? ? true : options[:reorder]

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File config.rb has 267 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'simple_crypt'


module Seek

Function add_selected_people has 59 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function add_selected_people() {
    var people = determine_selected_people();

    $j.each(people, function (index, value) {
        var person_id = value["person_id"];