Method studies_link_list has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def studies_link_list studies,sorted=true
    #FIXME: make more generic and share with other model link list helper methods
    studies=studies.select{|s| !s.nil?} #remove nil items
    return "<span class='none_text'>Not associated with any #{t('study').pluralize}</span>".html_safe if studies.empty?

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Method list_item_with_icon has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def list_item_with_icon(icon_type, item, caption, truncate_to, custom_tooltip=nil, size=nil)

Method recently_downloaded_item_logs_hash has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def recently_downloaded_item_logs_hash time=1.month.ago, number_of_item=10
    Rails.cache.fetch("download_activity_#{current_user_id}") do
      activity_logs = ActivityLog.no_spider.where(["action = ? AND created_at > ?", 'download', time]).order("created_at DESC")
      selected_activity_logs = []
      selected_items = []

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Method get_people_in_FG has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def get_people_in_FG contributor, fg_id=nil, is_white_list=nil, is_black_list=nil
    if is_white_list
      f_group = FavouriteGroup.where(["name = ? AND user_id = ?", "__whitelist__", contributor.user.id]).first
    elsif is_black_list
      f_group = FavouriteGroup.where(["name = ? AND user_id = ?", "__blacklist__", contributor.user.id]).first

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Method cytoscape_edge_elements has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def cytoscape_edge_elements edges
    cytoscape_edge_elements = []
    edges.each do |edge|
      source, target = edge.split('--')
      source.strip!

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Method tree_single_select_tag has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def tree_single_select_tag type, id, selected_item=nil, disabled_items=[], name=nil, html_options={:multiple => false, :size => 10, :style => "width:600px;"}

Method list_item_expandable_text has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def list_item_expandable_text attribute, text, length=200
    full_text  = text_or_not_specified(text, :description => false, :auto_link=>false)
    trunc_text = text_or_not_specified(text, :description => false, :auto_link=>false, :length=>length)
    #Don't bother with fancy stuff if not enough text to expand
    if full_text == trunc_text

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Method recently_added_item_logs_hash has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def recently_added_item_logs_hash time=1.month.ago, number_of_item=10
    Rails.cache.fetch("create_activity_#{current_user_id}") do
      item_types = Seek::Util.user_creatable_types.collect{|type| type.name} | [Project,Programme]
      activity_logs = ActivityLog.where(["action = ? AND created_at > ? AND activity_loggable_type in (?)", 'create', time, item_types]).order("created_at DESC")
      selected_activity_logs = []

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Method avatar has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def avatar(object, size=200, return_image_tag_only=false, url=nil, alt=nil, show_tooltip=true)

Method related_items_method has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def related_items_method(resource, item_type)
    if item_type == "TavernaPlayer::Run"
      method_name = 'runs'
    else
      method_name = item_type.underscore.pluralize

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Method policy_and_permissions_for_public_scope has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def policy_and_permissions_for_public_scope(policy, permissions, privileged_people, resource_name, updated_can_publish_immediately, send_request_publish_approval)

Method determine_submitter has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def determine_submitter object
    #FIXME: needs to be the creators for assets
    return object.owner if object.respond_to?("owner")
    result = object.contributor if object.respond_to?("contributor") && !object.kind_of?(Permission)
    if (result)

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Method allow_model_comparison has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def allow_model_comparison model,displayed_model,user=User.current_user
    return false unless model.is_a?(Model)
    return false unless model.can_download?(user)
    return false unless displayed_model.contains_sbml?
    return false unless model.versions.select{|v| v.contains_sbml?}.count > 1

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Method deep_parse has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def deep_parse(types, output, zip, index = [])
    content = "<ol>"
    i = 0
    types.each do |type|
      if type.is_a?(Array)

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Method list_item_with_icon has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def list_item_with_icon(icon_type, item, caption, truncate_to, custom_tooltip=nil, size=nil)
    list_item = "<li>"
    if icon_type.downcase == "flag"
      list_item += flag_icon(item.country)
    elsif icon_type == "data_file" || icon_type == "sop"

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Method delete_model_format has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def delete_model_format params
    id=params[:selected_model_format_id]
    model_format=ModelFormat.find(id)
    success=false
    if (model_format.models.empty?)

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Method new_strain has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def new_strain strain_params
    strain = Strain.new
    # to delete id hash which is saved in the hidden id field (automatically generated in form with fields_for)
    # try_block {
    #delete id hashes of genotypes/phenotypes

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Method determine_return_url_after_login has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def determine_return_url_after_login
    if !params[:called_from].blank? && !params[:called_from][:url].blank?
      return_to_url = params[:called_from][:url]
    elsif !params[:called_from].blank? && params[:called_from][:controller] != "sessions"
      if params[:called_from][:id].blank?

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Method submit_to_sycamore has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def submit_to_sycamore
    @model = Model.find_by_id(params[:id])
    @display_model = @model.find_version(params[:version])
    error_message = nil
    if !Seek::Config.sycamore_enabled

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Method destroy has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def destroy
    respond_to do |format|
      if @suggested_technology_type.can_destroy?
        title = @suggested_technology_type.label
        @suggested_technology_type.destroy

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