Function updateDisciplines has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateDisciplines() {
    discipline_text=''
    type="Discipline"
    discipline_ids=new Array();

Function updateOrganisms has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateOrganisms() {
    organism_text=''
    type="Organism"
    organism_ids=new Array();

Method indented_tree_child_options has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def indented_tree_child_options parent, depth=0, show_edit=true, show_delete=true, selected_id=nil, related_resource_type="Person",selected_display_items=nil, foldable=true
    result = []
    unless parent.children.empty?
      parent.children.sort { |a, b| a.title.downcase <=> b.title.downcase }.each do |child|
        display_style = (foldable==true) ? "display:none" : "display:block"

Method avatar has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def avatar(object, size=200, return_image_tag_only=false, url=nil, alt=nil, show_tooltip=true)
    alternative = ""
    title = get_object_title(object)
    if show_tooltip
      tooltip_text = (alt.nil? ? h(title) : alt)

Method fetch_preview has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def fetch_preview
    #trim the PubMed or Doi Id
    params[:key] = params[:key].strip() unless params[:key].blank?
    params[:publication][:project_ids].reject!(&:blank?).map! { |id| id.split(',') }.flatten!
    @publication = Publication.new(params[:publication])

Method included has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def self.included(base)
      raise "Only People can have roles" unless base==Person

      base.extend(ClassMethods)
      ROLES.each do |role|

Function toggleDynamicMenu has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

function toggleDynamicMenu(element) {

    function documentClickedHandler(event) {
        if (!event.element().hasClassName("dynamic_menu_li")) {
            switch (event.element().id) {

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Function updateOrganisms has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

function updateOrganisms() {
    organism_text='<ul class="related_asset_list">';    

    for (var i=0;i<organisms.length;i++) {
        organism=organisms[i];

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Method check_uniqueness_of_identifier_within_project has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def check_uniqueness_of_identifier_within_project
    if !doi.blank?
      existing = Publication.find_all_by_doi(doi) - [self]
      if !existing.empty?
        matching_projects = existing.collect(&:projects).flatten.uniq & projects

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Method process_queue has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def process_queue
    #including item_type in the order, encourages assets to be processed before users (since they are much quicker), due to tha happy coincidence
    #that User falls last alphabetically. Its not that important if a new authorized type is added after User in the future.
    todo = AuthLookupUpdateQueue.order("priority,item_type,id").limit(BATCHSIZE).collect do |queued|
      todo = queued.item

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Method send_announcement_emails has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def send_announcement_emails site_announcement, from_notifiee_id
    if Seek::Config.email_enabled
      NotifieeInfo.where(["id IN (?) AND receive_notifications=?", (from_notifiee_id .. (from_notifiee_id + BATCHSIZE)), true]).each do |notifiee_info|
        begin
          unless notifiee_info.notifiee.nil?

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Method value_for_key has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def value_for_key config_for_key, object
    facet_values = []
    value_from = config_for_key['value_from']
    value_from.split(',').each do |from|
      facet_value = object

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Method file_extension has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def file_extension
      if metadata.nil?
        nil
      else
        if metadata[:type].is_a?(Array)

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Method concat_roles_to_name has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def concat_roles_to_name grouped_people_by_access_type, creators, asset_managers
    creator_id_array = creators.collect{|c| c.id unless c.blank?}
    asset_manage_id_array = asset_managers.collect{|am| am.id unless am.blank?}
     grouped_people_by_access_type = grouped_people_by_access_type.reject{|key,value| key == Policy::DETERMINED_BY_GROUP}.each_value do |value|
       value.each do |person|

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Method list_item_visibility has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def list_item_visibility item,css_class="visibility_icon"
    title = ""
    html  = ""
    policy = item.policy

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Method windowed_pagination_links has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def windowed_pagination_links(pagingEnum, options)
    link_to_current_page = options[:link_to_current_page]
    always_show_anchors = options[:always_show_anchors]
    padding = options[:window_size]

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Method builder has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def builder
    saved_file=params[:saved_file]
    error=nil
    supported=false
    begin

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Method new has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def new
    @assay=Assay.new
    @assay.create_from_asset = params[:create_from_asset]
    study = Study.find(params[:study_id]) if params[:study_id]
    @assay.study = study if params[:study_id] if study.try :can_edit?

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Method index has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def index
    if (params[:discipline_id])
      @discipline=Discipline.find(params[:discipline_id])
      #FIXME: strips out the disciplines that don't match
      @people=Person.where(["disciplines.id=?",@discipline.id]).includes(:disciplines)

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Method create has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def create    

    if handle_upload_data
      @sop = Sop.new(params[:sop])
      @sop.policy.set_attributes_with_sharing params[:sharing], @sop.projects

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