Function goToSlide has 59 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        el.goToSlide = function(slideIndex, direction){
            // if plugin is currently in motion, ignore request
            if(slider.working || slider.active.index == slideIndex) return;
            // declare that plugin is in motion
            slider.working = true;

Class RdfRepository has 22 methods (exceeds 20 allowed). Consider refactoring.

Open

    class RdfRepository

        #provides a singleton instance of the configured repository
        def self.instance
          #TODO: in the future, when/if we support more repository flavours, the instance we return will need to be configurable

Function setup has 58 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var setup = function(){
            // wrap el in a wrapper
            el.wrap('<div class="bx-wrapper"><div class="bx-viewport"></div></div>');
            // store a namspace reference to .bx-viewport
            slider.viewport = el.parent();

Method parse_spreadsheet_xml has 58 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def parse_spreadsheet_xml(spreadsheet_xml)
        workbook = Workbook.new

        doc = LibXML::XML::Parser.string(spreadsheet_xml).parse
        doc.root.namespaces.default_prefix="ss"

Method initialize has 58 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def initialize file, xml=nil, to_populate=true, institution_id = nil
      @file = file

      @investigation = nil
      @study = nil

Method add_as_new has 57 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def add_as_new resource
      #FIXME: this method is too long 
      begin
        warning=nil
        warning_code=0

Method matching_models has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

  def matching_models

    results = {}

    if Seek::Config.solr_enabled && contains_extractable_spreadsheet?

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Method list_item_title has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

  def list_item_title resource, options={}
    cache_key = "rli_title_#{resource.cache_key}_#{resource.authorization_supported? && resource.can_manage?}"
    result = Rails.cache.fetch(cache_key) do
      title=options[:title]
      url=options[:url]

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Method update has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

  def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:model]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:model].delete(column_name)

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Method update has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

  def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:presentation]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:presentation].delete(column_name)

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Method new_object_based_on_existing_one has a Cognitive Complexity of 17 (exceeds 5 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"}

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Method create has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

  def create
    if handle_upload_data
      @model = Model.new(params[:model])

      @model.policy.set_attributes_with_sharing params[:sharing], @model.projects

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Method extract_as_table has a Cognitive Complexity of 17 (exceeds 5 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}'))]")

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Method find_or_new_substances has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    def find_or_new_substances(new_substances, known_substance_ids_and_types)
    result = []
    known_substances = known_substances known_substance_ids_and_types
    new_substances, known_substances = check_if_new_substances_are_known new_substances, known_substances
    result |= known_substances

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Method append_list_assay_organisms has 56 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def append_list_assay_organisms assay_organisms
    result=""

    organism=nil
    strain = nil

Method extended_xml has 56 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def extended_xml builder,object        
    
    submitter = determine_submitter object
    builder.tag! "submitter" do 
      api_partial(builder,submitter)

Class ContentBlob has 21 methods (exceeds 20 allowed). Consider refactoring.

Open

class ContentBlob < ActiveRecord::Base

  include Seek::ContentTypeDetection
  include Seek::PdfExtraction
  include Seek::MimeTypes

Function updateOrganisms has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateOrganisms() {
    organism_text='<ul class="related_asset_list">';    

    for (var i=0;i<organisms.length;i++) {
        organism=organisms[i];

Method submit_to_jws has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def submit_to_jws
    following_action=params.delete("following_action")
    error=nil

    #FIXME: currently we have to assume that a model with multiple files only contains 1 model file that would be executed on jws online, and only the first one is chosen

Function addSelectedOrganism has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

function addSelectedOrganism() {
    selected_option_index=$("possible_organisms").selectedIndex;
    selected_option=$("possible_organisms").options[selected_option_index];
    title=selected_option.text;
    id=selected_option.value;

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