Method set_parameters_for_sharing_form has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

Method new_object_based_on_existing_one has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def new_object_based_on_existing_one
    @existing_assay =  Assay.find(params[:id])
    @assay = @existing_assay.clone_with_associations
    params[:data_file_ids]=@existing_assay.data_file_masters.collect{|d|"#{d.id},None"}
    params[:related_publication_ids]= @existing_assay.related_publications.collect{|p| "#{p.id},None"}

Method update has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def update
    if params[:workflow]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:workflow].delete(column_name)
      end

Method create has 32 lines of code (exceeds 25 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

Method generate_triples has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def generate_triples subject, method, property,uri_or_literal,transformation,collection_transform,rdf_graph
        resource = subject.rdf_resource
        transform = transformation.strip unless transformation.nil?
        collection_transform = collection_transform.strip unless collection_transform.nil?
        items = subject.send(method)

Method create has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

   def create
      compound = params[:compound]
      compound_name =  compound[:title]

        unless compound_name.blank?

Method add has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def add
    if request.post?
      if params[:id]=="drag_search" #needs to create the SavedSearch resource first
        saved_search = SavedSearch.new(:user_id => current_user.id, :search_query => params[:search_query], :search_type => params[:search_type],:include_external_search=>params[:include_external_search]=="1")
        if SavedSearch.find_by_user_id_and_search_query_and_search_type_and_include_external_search(current_user,params[:search_query],params[:search_type],params[:include_external_search]=="1").nil? && saved_search.save

Method populate_db has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def populate_db data

      assay = nil
      assay_json = data["assay"]

Method paginate has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def paginate(*args)
      options=args.pop unless args.nil?
      options ||= {}                

      default_page = options[:default_page] || @default_page

Method extract_as_table has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def extract_as_table treatments_heading_row, sample_col, treatments_first_col,treatments_last_col,sheet
        table = []
        sheet_name = sheet.attributes["name"]
        cells = sheet.find("//ss:sheet[@name='#{sheet_name}']/ss:rows/ss:row/ss:cell[@row >= '#{(treatments_heading_row).to_s}' and (@column = '#{sample_col.to_s}' or (@column>='#{treatments_first_col.to_s}' and @column<='#{treatments_last_col.to_s}'))]")

Method fs_search_fields has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def fs_search_fields
    flds = studied_factors.collect do |fs|
      [fs.measured_item.title,
       fs.substances.collect do |sub|
         #FIXME: this makes the assumption that the synonym.substance appears like a Compound

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Function EventCache has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

var EventCache = function(){
    var listEvents = [];
    return {
        listEvents : listEvents,
        add : function(node, sEventName, fHandler){

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Method validates_associated has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def validates_associated(*associations)
    associations.each do |association|
      class_eval do
        validates_each(associations) do |record, associate_name, value|
          associates = record.send(associate_name)

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Function updateAssays has a Cognitive Complexity of 11 (exceeds 5 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];

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Function generate_json_data has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

function generate_json_data() {
    var cells = $j('td.selected_cell');
    var columns = $j('.col_heading.selected_heading').size();
    var headings;
    var rows = new Array();

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Method exp_conditions_search_fields has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def exp_conditions_search_fields
    flds = experimental_conditions.collect do |ec|
      [ec.measured_item.title,
       ec.substances.collect do |sub|
         #FIXME: this makes the assumption that the synonym.substance appears like a Compound

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Method summarize_permissions has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def summarize_permissions creators=[User.current_user.try(:person)], asset_managers = [], contributor=User.current_user.try(:person)
        #build the hash containing contributor_type as key and the people in these groups as value,exception:'Public' holds the access_type as the value
        people_in_group = {'Person' => [], 'FavouriteGroup' => [], 'WorkGroup' => [], 'Project' => [], 'Institution' => [], 'WhiteList' => [], 'BlackList' => [],'Network' => [], 'Public' => 0}
        #the result return: a hash contain the access_type as key, and array of people as value
        grouped_people_by_access_type = {}

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Method model_scales_list has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def model_scales_list model, list_item
    scales = model.scales
    if scales.empty?
      text_or_not_specified("")
    else

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Method csv_to_google_data has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def csv_to_google_data csv
    res = ""
    rows = CSV.parse(csv)
    rows.each_with_index do |row,i|
      if i==0

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Method specimen_row_data has a Cognitive Complexity of 11 (exceeds 5 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))

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