Method indented_tree_child_options has 8 arguments (exceeds 4 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

Function relativeRows has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

function relativeRows(minRow, maxRow, sheetNumber){
    var current_page = null;
    if (sheetNumber != null)
        current_page = currentPage(sheetNumber);

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Function additionalFieldForItem has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

function additionalFieldForItem(form_id, fs_or_ec_id){
    var elements =  $(form_id).getElements();
    var item;
    var substance_autocomplete;
    for (var i=0;i<elements.length;i++)

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Method send_subscription_mails has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def send_subscription_mails logs, frequency
    if Seek::Config.email_enabled
      #strip the logs down to those that are relevant
      logs.reject! do |log|
        log.activity_loggable.nil? || !log.activity_loggable.subscribable?

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Method people_i_may_know has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def people_i_may_know
    res=[]
    institutions.each do |i|
      i.people.each do |p|
        res << p unless p==self or res.include? p

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Method perform has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def perform
    item = item_type_name.constantize.find_by_id(item_id)
    unless item.nil?
      begin
        if item.rdf_repository_configured?

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Method check_url_content_type has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def check_url_content_type
    unless url.nil?
      begin
        response = RestClient.head url
        type = response.headers[:content_type] || ""

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Method get_all_as_json has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def self.get_all_as_json
    all_people = Person.order("ID asc")
    names_emails = all_people.collect{ |p| {"id" => p.id,
        "name" => (p.first_name.blank? ? (logger.error("\n----\nUNEXPECTED DATA: person id = #{p.id} doesn't have a first name\n----\n"); "(NO FIRST NAME)") : h(p.first_name)) + " " +
                  (p.last_name.blank? ? (logger.error("\n----\nUNEXPECTED DATA: person id = #{p.id} doesn't have a last name\n----\n"); "(NO LAST NAME)") : h(p.last_name)),

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Method fix_run_input_ports_mime_types has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def fix_run_input_ports_mime_types
      self.inputs.each do |input|
        input.metadata = {:size => nil, :type => ''} if input.metadata.nil?
        port = executed_workflow.input_ports.detect { |i| i.name == input.name }
        if port && !port.mime_type.blank?

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Method specimen_organism_list has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def specimen_organism_list organism,strain,culture_growth_type=nil,none_text="Not Specified"
    result=""
    result ="<span class='none_text'>#{none_text}</span>".html_safe if organism.nil?
    if organism
      result = link_to organism.title,organism,{:class => "assay_organism_info"}

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Method recent_changes_hash has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def recent_changes_hash

    item_hash=classify_for_tabs(Person.order('updated_at DESC').limit(RECENT_SIZE))
    item_hash.merge! classify_for_tabs(Project.order('updated_at DESC').limit(RECENT_SIZE))

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Method fancy_multiselect has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def fancy_multiselect object, association, options = {}
      if options[:project_possibilities]  &&  options[:other_projects_checkbox]
        type = object.class.name.underscore
        default_checked = Seek::Config.is_virtualliver ? true : false
        check_box_and_alternative_list = "".html_safe

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Method list_organisms_and_strains has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def list_organisms_and_strains organism_and_strains, none_text="Not specified"
    result=""
    result="<span class='none_text'>#{none_text}</span>" if organism_and_strains.empty?
    organism_and_strains.each do |os|
      organism=os[0]

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Method rows_to_flot_data has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def rows_to_flot_data rows
    data = {}
    labels = []
    rows.each_with_index do |row,y|
      t=nil

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Method internationalized_resource_name has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def internationalized_resource_name resource_type,pluralize=true
    resource_type = resource_type.singularize
    if resource_type == "Speciman"
      result = t('biosamples.sample_parent_term')
    elsif resource_type == "Assay"

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Method simulate has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

 def simulate
    error=nil
    begin
      if @display_model.is_jws_supported?
        @modelname = Seek::JWS::Simulator.new.simulate(@display_model.jws_supported_content_blobs.first)

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Method existing_strains has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def existing_strains
      strains_of_organisms = []
      organisms = []
      if params[:organism_ids]
        organism_ids = params[:organism_ids].split(',')

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Method update has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def update
    
    # extra check required to see if any avatar was actually selected (or it remains to be the default one)
    avatar_id = params[:project].delete(:avatar_id).to_i
    @project.avatar_id = ((avatar_id.kind_of?(Numeric) && avatar_id > 0) ? avatar_id : nil)

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Method auth has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def auth
    action = translate_action(action_name)
    unless is_auth?(@sweep, action)
      if User.current_user.nil?
        flash[:error] = "You are not authorized to #{action} this Sweep, you may need to login first."

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Method compare_versions has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def compare_versions
    if params[:file_id]
      @blob1 = @display_model.sbml_content_blobs.find{|b| b.id.to_s == params[:file_id]}
    else
      @blob1 = @display_model.sbml_content_blobs.first

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