Function setTheDivStyle has 42 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function setTheDivStyle() {
if(!readCookie('name_panel')) {
// if cookie not found display the div and create the cookie
//document.getElementById("name_panel").style.display="block";
//createCookie('name_panel', 1);  // 1 day = 24 hours persistence

Method specimen_row_data has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def specimen_row_data specimen
    id_column = Seek::Config.is_virtualliver ? 8 : 6
    creators = []
    specimen.creators.each do |creator|
      creators << link_to(h(creator.name), person_path(creator.id))

Method tree_editor_display has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def tree_editor_display type, show_edit=true, show_delete=true, selected_id=nil, related_resource_type="Person",selective_display=false, foldable=false

    selected_display_items = nil

    if selected_id && selective_display

Method send_policy_data has 41 lines of code (exceeds 25 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])
    

Method update_rdf has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        def update_rdf(item)
          if configured?
            connect_to_repository
            graphs = rdf_graph_uris(item)
            rdf_file_path = last_rdf_file_path(item)

Method populate_treatment has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def populate_treatment treatment_json, specimen=nil, sample=nil

        start_value = treatment_json["start value"]
        end_value = treatment_json["end value"]
        standard_deviation = treatment_json["standard deviation"]

Method clone_versioned_model has 41 lines of code (exceeds 25 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) ||

Function updateAssays has 40 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateAssays() {
    assay_text = '<ul class="related_asset_list">'
    for (var i=0;i<assays_array.length;i++) {
        assay=assays_array[i];
        title=assay[0];

Method tag_with has 40 lines of code (exceeds 25 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

Function displayNormal has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

function displayNormal() {
    var xmlHttp;
    try {  // Firefox, Opera 8.0+, Safari  
        xmlHttp = new XMLHttpRequest(); 
        if (xmlHttp.overrideMimeType) {

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Method dump_tmp_io_object_to_file has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def dump_tmp_io_object_to_file
    raise Exception.new("You cannot define both :data content and a :tmp_io_object") unless @data.nil? || @tmp_io_object.nil?
    t1 = Time.now
    unless @tmp_io_object.nil?
      begin

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Method set_parameters_for_sharing_form has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def set_parameters_for_sharing_form object=nil
    object ||= eval "@#{controller_name.singularize}"
    policy = nil
    policy_type = ""

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Method policy_to_people_group has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def policy_to_people_group people_in_group, contributor=User.current_user.person
      if sharing_scope == Policy::ALL_SYSMO_USERS
         people_in_network = get_people_in_network access_type
         people_in_group['Network'] |= people_in_network unless people_in_network.blank?
      elsif sharing_scope == Policy::EVERYONE

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Method resource_title_draggable_avatar has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def resource_title_draggable_avatar resource, version=nil

    icon=""
    image=nil
    if resource.avatar_key

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Method people_by_project_options has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def people_by_project_options(projects)
    options = ""
    projects.each do |project|
      project_options = "<optgroup id=#{project.id} title=\"#{h project.title}\" label=\"#{h truncate(project.title)}\">"
      project.people.sort{|a,b| (a.last_name.nil? ? nil : a.last_name.capitalize) <=> (b.last_name.nil? ? nil : b.last_name.capitalize)}.each do |person|

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Method date_as_string has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def date_as_string date,show_time_of_day=false,year_only_1st_jan=false
    #for publications, if it is the first of jan, then it can be assumed it is just the year (unlikely have a publication on New Years Day)
    if (year_only_1st_jan && !date.blank? && date.month==1 && date.day==1)
      str=date.year.to_s
    else

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Method associate_organism has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def associate_organism(organism,strain_id=nil,culture_growth_type=nil,tissue_and_cell_type_id="0",tissue_and_cell_type_title=nil)
    organism = Organism.find(organism) if organism.kind_of?(Numeric) || organism.kind_of?(String)
    strain=organism.strains.find_by_id(strain_id)
    assay_organism=AssayOrganism.new(:assay=>self,:organism=>organism,:culture_growth_type=>culture_growth_type,:strain=>strain)

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Method find_and_filter_workflows has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def find_and_filter_workflows
    find_assets

    # Has the user cleared the search box? - return all items.
    uploader = params[:uploader_id]

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Method update has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def update
    @person.disciplines.clear if params[:discipline_ids].nil?

    # extra check required to see if any avatar was actually selected (or it remains to be the default one)
    

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Method check_for_override has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def check_for_override context, options
      unless options[:seek_template].nil?
        value = @@alternative_map[{:controller => context.controller_name, :seek_template => options[:seek_template].to_s}]
        unless value.nil?
          options[:template]=value

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