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

Open

  def create
    @sample = Sample.new(params[:sample])
    # create new specimen only for combined form
    is_new_spec = params[:sample][:specimen_id].nil? ? true : false

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

Open

      def self.is_authorized?(action, thing_type, thing, user=nil)

        # initially not authorized, so if all tests fail -
        # safe result of being not authorized will get returned
        is_authorized = false

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Method populate_sample has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.

Open

    def populate_sample sample_json, specimen, assay=nil


        sample_title = sample_json["title"]
        sample_type = sample_json["type"]

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Method dortmund_hengstler_mapping has 123 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def dortmund_hengstler_mapping

      age_regex = /(\d+-?\d*)\s*(day|week|month|year)s?/i
      treatment_regex = /(\d*\.?\d*)\s*(\w+\/\w+)\s*([\w\.\s,']*),?\s+([\w\.]*)/
      incubation_time_regex = /(\d+\.?\d*)(\w{1})/

File person.rb has 366 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'grouped_pagination'

class Person < ActiveRecord::Base

  include Seek::Rdf::RdfGeneration

Method included has a Cognitive Complexity of 32 (exceeds 5 allowed). Consider refactoring.

Open

      def self.included klass
        klass.class_eval do
          include Seek::Search::CommonFields

          searchable do

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Method set_default_subscriptions has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.

Open

  def set_default_subscriptions projects
    unless projects.empty?
      Person.scoped(:include => :project_subscriptions).each do |person|
        project_subscriptions = person.project_subscriptions
        project_subscriptions.each do |ps|

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File people_controller.rb has 357 lines of code (exceeds 250 allowed). Consider refactoring.

Open

class PeopleController < ApplicationController

  include Seek::AnnotationCommon
  include Seek::Publishing::PublishingCommon
  include Seek::Publishing::GatekeeperPublish

Method submit_to_jws has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.

Open

  def submit_to_jws
    following_action=params.delete("following_action")
    error=nil

    #FIXME: currently we have to assume that a model with multiple files only contains 1 model file that would be executed on jws online, and only the first one is chosen

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Class Policy has 34 methods (exceeds 20 allowed). Consider refactoring.

Open

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

Method list_samples_and_assay_organisms has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.

Open

  def list_samples_and_assay_organisms attribute, assay_samples, assay_organisms, html_options={}, none_text="Not Specified"

    result= "<p class='#{html_options[:class]}' id='#{html_options[:id]}'> <b>#{attribute}</b>: "

    result +="<span class='none_text'>#{none_text}</span>" if assay_samples.blank? and assay_organisms.blank?

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Method perform_search has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.

Open

  def perform_search
    @search_query = params[:search_query]
    @search=@search_query # used for logging, and logs the origin search query - see ApplicationController#log_event
    @search_query||=""
    @search_type = params[:search_type]

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Class ApplicationController has 33 methods (exceeds 20 allowed). Consider refactoring.

Open

class ApplicationController < ActionController::Base

  include Seek::Errors::ControllerErrorHandling
  include Seek::EnabledFeaturesFilter
  include Recaptcha::Verify

Class BioSamples has 33 methods (exceeds 20 allowed). Consider refactoring.

Open

    class BioSamples

    attr_reader :investigation, :study, :assay, :assay_class, :assay_type,
                :units, :treatments, :organisms, :strains, :culture_growth_type, :tissue_and_cell_types,
                :specimens, :samples,  :specimen_names, :sample_names, :treatments,:treatments_text,

Method create_or_update_attributions has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.

Open

  def self.create_or_update_attributions(resource, attributions_from_params, predicate = Relationship::ATTRIBUTED_TO)

    # added this branching on .nil? because of the danger of loosing all attributions for a model (for example) if due to an incomplete post request attributions is nil
    # the former code interpreted a nil parameter as an empty list => remove all attributions from an asset
    unless attributions_from_params.nil?

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Method dortmund_bcat_ko_mapping has 102 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def dortmund_bcat_ko_mapping

      age_regex = /(\d+-?\d*)\s*(day|week|month|year)s?/i
      treatment_substance_regex = /.*\((control|treated)\s?=\s?(.*)\)/i
      treatment_concentration_unit_regex = /(\d*[,\.]?\d*)\s*([\w\s\/]*).*$/

Function dragObject has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

function dragObject(element, attachElement, lowerBound, upperBound, startCallback, moveCallback, endCallback, attachLater)
{
  if(typeof(element) == "string")
    element = document.getElementById(element);
  if(element == null)

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Function dragObject has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

function dragObject(element, attachElement, lowerBound, upperBound, startCallback, moveCallback, endCallback, attachLater)
{
  if(typeof(element) == "string")
    element = document.getElementById(element);
  if(element == null)

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Method update has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

  def update
    group_name = white_list(params[:favourite_group_name])
    found = FavouriteGroup.where(:name => group_name, :user_id => current_user.id).first
    
    # if the found group with the same is the current one - that's fine; otherwise - can't rename a group with such new name 

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Method included has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

      def self.included klass
        klass.class_eval do
          searchable do
            text :title do
              if self.respond_to?(:title)

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