Method asset_report has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

  def asset_report
    @no_sidebar=true
    project_assets = @project.assets | @project.assays | @project.studies | @project.investigations
    @types=[DataFile,Model,Sop,Presentation,Investigation,Study,Assay]
    @public_assets = {}

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Method sharing_params_to_policy has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

  def sharing_params_to_policy params=params
      policy =Policy.new()
      policy.sharing_scope = params["sharing_scope"].to_i unless params[:sharing_scope].blank?
      policy.access_type = params[:access_type].blank? ? 0 : params["access_type"].to_i
      policy.use_whitelist = params["use_whitelist"] == 'true' ? true : false

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File api_helper.rb has 302 lines of code (exceeds 250 allowed). Consider refactoring.

Open

module ApiHelper
  
  def xml_root_attributes
    { "xmlns" => "http://www.sysmo-db.org/2010/xml/rest",
      "xmlns:xsi" => "http://www.w3.org/2001/XMLSchema-instance",

File explicit_versioning.rb has 299 lines of code (exceeds 250 allowed). Consider refactoring.

Open

module Jits
  module Acts
    # Based heavily on the acts_as_versioned plugin
    module ExplicitVersioning
      CALLBACKS = [:sync_latest_version]

Class PeopleController has 27 methods (exceeds 20 allowed). Consider refactoring.

Open

class PeopleController < ApplicationController

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

Method populate_sample has 78 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def populate_sample sample_json, specimen, assay=nil


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

Function addSelected has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

function addSelected(resource_type, source) {
    if (source == "target") {
        for(var key in checkedTargetMap[resource_type]) {
            if (allLinks[resource_type][key] == true) {

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Method permissions_to_people_group has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

  def permissions_to_people_group permissions, people_in_group
      permissions.each do |permission|
        contributor_id = permission.contributor_id
        access_type = permission.access_type
        case permission.contributor_type

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Method do_projects_belong_to_project_manager_projects has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

  def do_projects_belong_to_project_manager_projects
      if (params[:person] and params[:person][:work_group_ids])
        if User.project_manager_logged_in? && !User.admin_logged_in?
          projects = []
          params[:person][:work_group_ids].each do |id|

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Method edit_tag has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

  def edit_tag
    if request.post?
      @tag=TextValue.find(params[:id])
      replacement_tags = []

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Method clone_versioned_model has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

          def clone_versioned_model(orig_model, new_model, process_file_columns=true)
            self.versioned_attributes.each do |key|
              # Make sure to ignore file columns, white list columns, timestamp columns and any other ignore columns
              unless self.file_columns.include?(key) ||
                     self.white_list_columns.include?(key) ||

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Method duesseldorf_bode_mapping has 76 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def duesseldorf_bode_mapping

      concentration_regex = /(\d*,?\.?\d*).*/
      gene_modification_regex = /([\w\d]+)([\/+-]+)/

Class Project has 26 methods (exceeds 20 allowed). Consider refactoring.

Open

class Project < ActiveRecord::Base

  include Seek::Rdf::RdfGeneration
  include Seek::Rdf::ReactToAssociatedChange

Function Position has 73 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

Function Position has 73 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

Method display_single_entry has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  def display_single_entry entry
      html=''
      unless entry.blank?
          #get the link of the entry
          entry_link = entry.url

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Method delete_or_cancel_button has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  def delete_or_cancel_button(run, redirect_to)
    if run.can_delete?
      if run.complete?
      # Delete
        unless current_user.guest?

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Method forgot_password has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  def forgot_password    
    if request.get?
      # forgot_password.rhtml
    elsif request.post?      
      user = User.find_by_login(params[:login])

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Method update has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  def update
    if params[:workflow]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:workflow].delete(column_name)
      end

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Method new_version has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

  def new_version
    if handle_upload_data
      comments=params[:revision_comment]

      respond_to do |format|

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