Function addAll has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

function addAll(resource_type, source) {

    if (source == "target") {
        for(var key in allLinks[resource_type]) {
            $(resource_type +"_" + key + "_target_row").hide();

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Method samples_link_list has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

  def samples_link_list samples
    #FIXME: make more generic and share with other model link list helper methods
    samples=samples.select{|s| !s.nil?} #remove nil items
    return "<span class='none_text'>Not Specified</span>".html_safe if samples.empty?

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Method create has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

  def create
    if handle_upload_data

      @workflow = Workflow.new params[:workflow]
      @workflow.policy.set_attributes_with_sharing params[:sharing], @workflow.projects

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Method upload_from_email has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

  def upload_from_email
    if current_user.is_admin? && Seek::Config.admin_impersonation_enabled
      User.with_current_user Person.find(params[:sender_id]).user do
        if handle_upload_data
          @data_file = DataFile.new params[:data_file]

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Method send_policy_data has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

  def send_policy_data
    request_type = white_list(params[:policy_type])
    entity_type = white_list(params[:entity_type])
    entity_id = white_list(params[:entity_id])
    

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Method open_id_authentication has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

  def open_id_authentication(identity_url)
    # Pass optional :required and :optional keys to specify what sreg fields you want.
    # Be sure to yield registration, a third argument in the #authenticate_with_open_id block.
    authenticate_with_open_id(identity_url,        
        :required => [:email, :fullname,

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Method get_selected_projects has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

  def get_selected_projects project_ids, resource_name
    if (resource_name == 'study') and (!project_ids.blank?)
      investigation = Investigation.find_by_id(project_ids.to_i)
      projects = investigation.nil? ? [] : investigation.projects

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Method handle_download has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def handle_download disposition='attachment', image_size=nil
      if @content_blob.url.blank?
        if @content_blob.file_exists?
          if image_size && @content_blob.is_image?
            @content_blob.copy_image

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Method tag_with has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def tag_with tags, attr="tag", owner=User.current_user,owned_tags_only=false
      tags = Array(tags)
      #FIXME: yuck! - this is required so that self has an id and can be assigned to an Annotation.annotatable
      return if self.new_record? && !self.save

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Method managers has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

      def managers
        #FIXME: how to handle projects as contributors - return all people or just specific people (pals or other role)?
        people=[]
        unless self.contributor.nil?
          people << self.contributor.person if self.contributor.kind_of?(User)

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Method parse_xml_with_extension has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def parse_xml_with_extension(article)
          doi_record = parse_xml_without_extension(article)
          begin
            #bug fix for empty/missing book title
            doi_record.journal ||= article.find_first("//book_metadata/titles/title").try(&:content)

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Method add_breadcrumbs has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def add_breadcrumbs
      #Home
      add_breadcrumb "Home", :root_path
      #process for nested attributes
      if controller_name == 'studied_factors'

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Method new_or_update_mapping_links has a Cognitive Complexity of 16 (exceeds 5 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"]

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Method duesseldorf_bode_mapping has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def duesseldorf_bode_mapping

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

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Function detect_browser has 50 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function detect_browser(){
    var browser = new Object();
    browser.name  = navigator.appName;
    browser.fullVersion  = ''+parseFloat(navigator.appVersion);
    browser.majorVersion = parseInt(navigator.appVersion,10);

Method update has 50 lines of code (exceeds 25 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 

Method explicit_versioning has 50 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        def explicit_versioning(options = {}, &extension)
          # don't allow multiple calls
          return if self.included_modules.include?(Jits::Acts::ExplicitVersioning::ActMethods)

          send :include, Jits::Acts::ExplicitVersioning::ActMethods

Method empty_mapping has 48 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def empty_mapping # defines basic mapping to start with, not that useful for the real parsing business ;-)
      {
          :name => "",
          :data_row_offset => 1, # add this to the row of a header column to get to row with the first data element

Method jena_mapping has 48 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def jena_mapping
      {
          :name => "jena",
          :data_row_offset => 2,

Method to_presentation_version has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def to_presentation_version
      Presentation::Version.new.tap do |presentation_version|
        presentation_version.attributes.keys.each do |attr|
          presentation_version.send("#{attr}=", send("#{attr}")) if respond_to? attr and attr!="id"
        end

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