Method authorization_permissions has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

      def authorization_permissions user=User.current_user
        @@expected_true_value ||= ActiveRecord::Base.connection.quoted_true.gsub("'","")
        permissions = AuthPermissions.new
        user_id = user.nil? ? 0 : user.id
        if Seek::Config.auth_lookup_enabled && self.class.lookup_table_consistent?(user_id)

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Method find_treatment_row_and_columns_in_sheet has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

      def find_treatment_row_and_columns_in_sheet sheet
        sheet_name = sheet.attributes["name"]
        treatment_cell_element = sheet.find("//ss:sheet[@name='#{sheet_name}']/ss:rows/ss:row/ss:cell").find do |cell|
          cell.content.match(/treatment.*/i)
        end

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Method merge_conditions has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def merge_conditions(*conditions)
      segments = []

      conditions.each do |condition|
        unless condition.blank?

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Method acts_as_asset has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

      def acts_as_asset
        attr_accessor :parent_name
        include Seek::Taggable

        acts_as_scalable

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Method update_subscription_job_if_study_or_assay has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def update_subscription_job_if_study_or_assay
    if self.kind_of?(Study) && self.investigation_id_changed?
      #update subscriptions for study
      old_investigation_id = self.investigation_id_was
      old_investigation = Investigation.find_by_id old_investigation_id

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Method roles has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def roles(project=nil)
      project_id = (project.is_a?(Project)) ? project.id : project.to_i
      role_names.select do |role_name|
        if self.class.is_project_dependent_role?(role_name)
          if project_id.nil?

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Method fix_run_output_ports_mime_types has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

def fix_run_output_ports_mime_types(run)
  run.outputs.each do |output|
    output.metadata = {:size => nil, :type => ''} if output.metadata.nil?
    port = run.executed_workflow.output_ports.detect { |o| o.name == output.name }
    if port && !port.mime_type.blank?

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Function addOrganism has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

function addOrganism(title,id,strain_info,strain_id,culture_growth,t_id,t_title) {

Function roundRectangleIntersectLine has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

        x, y, nodeX, nodeY, width, height, padding) {

Method image_tag_for_key has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def image_tag_for_key(key, url=nil, alt=nil, html_options={}, label=key.humanize, remote=false, size=nil)

Method tree_editor_display has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def tree_editor_display type, show_edit=true, show_delete=true, selected_id=nil, related_resource_type="Person",selective_display=false, foldable=false

Method generate_triples has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

      def generate_triples subject, method, property,uri_or_literal,transformation,collection_transform,rdf_graph

Function checkItem has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

function checkItem(id, source, resource_type) {
    if (source == "target") {
        if (allLinks[resource_type][id] == true){
            checkedTargetMap[resource_type][id] = false;
            allLinks[resource_type][id] = false;

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Function updateDataFiles has a Cognitive Complexity of 8 (exceeds 5 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];

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Function updatePublications has a Cognitive Complexity of 8 (exceeds 5 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];

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Function deactivate_previous_tab has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

function deactivate_previous_tab(tab_element){
        var previous_active_tab = tab_element.up("ul.tabbernav").getElementsByClassName('tabberactive')[0];
        previous_active_tab.className = '';
        //Then hide the content of the tab
        var scale_and_type = previous_active_tab.childNodes[0].className;

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Method to_presentation has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def to_presentation
    presentation_attrs = attributes.delete_if { |k, v| !(::Presentation.new.attributes.include?(k))}

    Presentation.new(presentation_attrs).tap do |presentation|
      DataFile.reflect_on_all_associations.select { |a| [:has_many, :has_and_belongs_to_many, :has_one].include?(a.macro) && !a.through_reflection }.each do |a|

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Function annotation has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

function annotation(id, type, sheet_number, cell_range, content, date_created) {

Method resource_tab_item_name has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def resource_tab_item_name resource_type,pluralize=true
    resource_type = resource_type.singularize
    if resource_type == "Speciman"
      result = t('biosamples.sample_parent_term')
    elsif resource_type == "Assay"

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Method get_people_in_network has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def get_people_in_network access_type
    people_in_network = [] #id, name, access_type
    projects = Project.all
    projects.each do |project|
      project.people.each do |person|

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