Function validateResourceFields has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function validateResourceFields(is_new_file, resource_name, is_managed) {
    // check if sharing rights are defined
    if (!($(document.getElementById('sharing_scope_0')).checked) &&
        !($(document.getElementById('sharing_scope_2')).checked) &&
        !($(document.getElementById('sharing_scope_4')).checked))

Method cytoscape_node_elements has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def cytoscape_node_elements nodes
    cytoscape_node_elements = []
    nodes.each do |node|
      item_type, item_id = node.split('_')
      item = item_type.constantize.find_by_id(item_id)

Method list_samples_and_assay_organisms has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def list_samples_and_assay_organisms attribute, assay_samples, assay_organisms, html_options={}, none_text="Not Specified"

    result= "<p class='#{html_options[:class]}' id='#{html_options[:id]}'> <b>#{attribute}</b>: "

    result +="<span class='none_text'>#{none_text}</span>" if assay_samples.blank? and assay_organisms.blank?

Method update has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def update
    data_file_ids = (params[:sample_data_file_ids].nil? ? [] : params[:sample_data_file_ids].reject(&:blank?)) || []
    model_ids = (params[:sample_model_ids].nil? ? [] : params[:sample_model_ids].reject(&:blank?)) || []
    sop_ids = (params[:sample_sop_ids].nil? ? [] : params[:sample_sop_ids].reject(&:blank?)) || []
    @sample.attributes = params[:sample]

Method paginate_after_fetch has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def paginate_after_fetch(collection, *args)
      options=args.pop unless args.nil?
      options ||= {}
      reorder = options[:reorder].nil? ? true : options[:reorder]

Function onTouchEnd has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var onTouchEnd = function(e){
            slider.viewport.unbind('touchmove', onTouchMove);
            var orig = e.originalEvent;
            var value = 0;
            // record end x, y positions

Function updateEvents has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateEvents() {
    event_text = '<ul class="related_asset_list">'
    for (var i = 0; i < events_array.length; i++) {
        var event = events_array[i];
        var title = event[0];

Function getViewportHeight has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var getViewportHeight = function(){
            var height = 0;
            // first determine which children (slides) should be used in our height calculation
            var children = $();
            // if mode is not "vertical" and adaptiveHeight is false, include all children

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

Open

  def set_attributes_with_sharing sharing, projects
    # if no data about sharing is given, it should be some user (not the owner!)
    # who is editing the asset - no need to do anything with policy / permissions: return success
    self.tap do |policy|
      if sharing

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

Open

    def populate_db data

      assay = nil
      assay_json = data["assay"]

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}'))]")

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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