Function validateResourceFields has a Cognitive Complexity of 15 (exceeds 5 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))

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Function detect_browser has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

function detect_browser(){
    var browser = new Object();
    browser.name  = navigator.appName;
    browser.fullVersion  = ''+parseFloat(navigator.appVersion);
    browser.majorVersion = parseInt(navigator.appVersion,10);

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Method authorize_related_items has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  def authorize_related_items(related)
    related.each do |key, res|
      res[:items].uniq!
      res[:items].compact!
      unless res[:items].empty?

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Method process_permissions has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  def process_permissions permissions, resource_name, display_no_access=false
    #remove the permissions with access_type=NO_ACCESS
    permissions.select!{ |p| p.access_type != Policy::NO_ACCESS } unless display_no_access

    html = ''

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Method recent_project_changes_hash has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  def recent_project_changes_hash

    projects=current_user.person.projects
    
    people=Person.order('updated_at DESC')

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Method filter_feeds_entries_with_chronological_order has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

  def filter_feeds_entries_with_chronological_order feeds, number_of_entries=10
    filtered_entries = []
    unless feeds.blank?
      feeds.each do |feed|
         entries = try_block{feed.entries}

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Method update has a Cognitive Complexity of 15 (exceeds 5 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]

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Method update has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

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

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Method update_params_for_batch has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

      def update_params_for_batch(params)
        data = []
        data_urls = []
        original_filenames = []
        make_local_copy = []

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Method builder_content has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

      def builder_content content_blob
          filepath=content_blob.filepath

          #this is necessary to get the correct filename and especially extension, which JWS relies on
          tmpfile = Tempfile.new([content_blob.original_filename,File.extname(content_blob.original_filename)])

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Method initialize has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

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

      @investigation = nil
      @study = nil

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Method populate_db has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def populate_db data

      assay = nil
      assay_json = data["assay"]

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Method spreadsheet_contents_for_search has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

      def spreadsheet_contents_for_search obj=self
        if obj.content_blob.is_extractable_spreadsheet?
          content = Rails.cache.fetch("#{obj.content_blob.cache_key}-ss-content-for-search") do
            begin
              xml=obj.spreadsheet_xml

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Method is_authorized? has 47 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.is_authorized?(action, thing_type, thing, user=nil)

        # initially not authorized, so if all tests fail -
        # safe result of being not authorized will get returned
        is_authorized = false

Function addSelected has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function addSelected(resource_type, source) {
    if (source == "target") {
        for(var key in checkedTargetMap[resource_type]) {
            if (allLinks[resource_type][key] == true) {

Method create has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    params[:assay_class_id] ||= AssayClass.for_type("experimental").id
    @assay        = Assay.new(params[:assay])

    organisms     = params[:assay_organism_ids] || []

Method update has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def update

    #FIXME: would be better to resolve the differences, rather than keep clearing and reading the assets and organisms
    #DOES resolve differences for assets now
    organisms             = params[:assay_organism_ids]||[]

Method create has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @sample = Sample.new(params[:sample])
    # create new specimen only for combined form
    is_new_spec = params[:sample][:specimen_id].nil? ? true : false

Method find_and_authorize_requested_item has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def find_and_authorize_requested_item
    begin
      name = self.controller_name.singularize
      action = translate_action(action_name)

Function addSelectedOrganism has 45 lines of code (exceeds 25 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;