Method preview_permissions has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def preview_permissions
      policy = sharing_params_to_policy
      current_person = User.current_user.try(:person)
      contributor_person = (params['is_new_file'] == 'false') ?  User.find_by_id(params['contributor_id'].to_i).try(:person) : current_person
      creators = (params["creators"].blank? ? [] : ActiveSupport::JSON.decode(params["creators"])).uniq

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Method extract_workflow_metadata has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def extract_workflow_metadata
    @t2flow = T2Flow::Parser.new.parse(@workflow.content_blob.data_io_object.read)

    @workflow.title = @t2flow.annotations.titles.last unless @t2flow.annotations.titles.last.blank?
    @workflow.description = @t2flow.annotations.descriptions.last

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Method destroy has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def destroy
    object=params[:class].capitalize.constantize.find(params[:id])
    if object && object.is_a?(Sample)
       specimen = object.specimen
       id_column = Seek::Config.is_virtualliver ? 8 : 6

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Method auth has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def auth
      # Skip certain auth if run is embedded
      if @run.embedded
        if ['cancel','read_interaction','write_interaction'].include?(action_name)
          return true

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Method uri_for_object has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def self.uri_for_object(resource_obj, *args)
      options = args.extract_options!
      # defaults:
      options.reverse_merge!(:params => nil,
                             :sub_path => nil)

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Method filter_size has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def filter_size size
    max_size=1500
    matches = size.match /([0-9]+)x([0-9]+).*/
    if matches
      width = matches[1].to_i

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Method add_roles has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def add_roles roles
      new_mask = self.roles_mask || 0
      roles.each do |role_details|
        rolename = role_details[0]
        raise UnknownRoleException.new("Unrecognised role name #{rolename}") unless ROLES.include?(rolename)

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Function updatePublications has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updatePublications() {
    publication_text='<ul class="related_asset_list">'
    
    for (var i=0;i<publication_array.length;i++) {        
        publication=publication_array[i];

Function updateModels has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateModels() {
    model_text='<ul class="related_asset_list">';
    type="Model";
    model_ids=new Array();

Function updateDataFiles has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateDataFiles() {
    data_file_text='<ul class="related_asset_list">'
    
    for (var i=0;i<data_files_assets.length;i++) {        
        data_file=data_files_assets[i];

Method included has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.included klass
        klass.class_eval do
          include Seek::Search::CommonFields

          searchable do

Method populate_assay has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def populate_assay assay_json, filename

      investigation_title = assay_json["investigation title"]
      assay_type_title = assay_json["assay type title"]
      study_title = assay_json["study title"]

Function parse has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function parse(nodes, tree, id) {
        for (var i = 0; i < nodes.length; i++) {
            if (1 != nodes[i].nodeType) {
                continue;
            }

Function updateSops has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateSops() {
    sop_text='<ul class="related_asset_list">';

    sop_ids=new Array();

Method create has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    if handle_upload_data
      @presentation = Presentation.new(params[:presentation])

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

Method perform_search has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def perform_search
    @search_query = params[:search_query]
    @search=@search_query # used for logging, and logs the origin search query - see ApplicationController#log_event
    @search_query||=""
    @search_type = params[:search_type]

Method edit_tag has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def edit_tag
    if request.post?
      @tag=TextValue.find(params[:id])
      replacement_tags = []

Method create has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @publication = Publication.new(params[:publication])
    @publication.pubmed_id=nil if @publication.pubmed_id.blank?
    @publication.doi=nil if @publication.doi.blank?
    pubmed_id,doi = preprocess_doi_or_pubmed @publication.pubmed_id,@publication.doi

Consider simplifying this complex logical expression.

Open

          unless sample.specimen == specimen &&
              sample.sample_type == sample_type &&
              (sample.tissue_and_cell_types.member?(tissue_and_cell_type) || tissue_and_cell_type_title == "") &&
              sample.donation_date == Time.zone.parse(donation_date).utc &&
              sample.institution == institution &&

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

Open

        var init = function(){
            // merge user-supplied options with the defaults
            slider.settings = $.extend({}, defaults, options);
            // parse slideWidth setting
            slider.settings.slideWidth = parseInt(slider.settings.slideWidth);