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

Open

    def set_smtp_settings (field, value)
      if [:password, :user_name, :authentication].include? field.to_sym
        if value.blank?
          value = nil
        end

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Avoid deeply nested control flow statements.

Open

                    if self.respond_to?(action_method) && !self.send(action_method)
                      result = false
                      errors.add(:base,"You are not permitted to change #{reflection.name} on #{self.class.name.underscore.humanize}-#{id} without #{action} rights")
                      break
                    end

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

Open

        def bio_samples_population institution_id=nil, to_populate=true
          begin
            if content_blob.is_extractable_spreadsheet?

              bio_samples = nil

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

Open

    def hunt_for_field_values_mapped sheet, field_name, mapping, probing_num_rows = false
      field_values = hunt_for_field_values sheet, mapping[field_name][:column], probing_num_rows
      if field_values && !field_values.empty?

        if probing_num_rows

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

Open

    def basic_auth url, username,password, include_data=true
      
      #This block is to ensure that only urls are encoded if they need it.
      #This is to prevent already encoded urls being re-encoded, which can lead to % being replaced with %25.
      begin

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

Open

      def treatments
        Seek::Data::Treatments #this is just to load the class, incase it is already in the cache. Otherwise an underfined class/module error may occur
        Rails.cache.fetch("treatments_#{content_blob.cache_key}") do
          begin
            if content_blob.is_extractable_spreadsheet?

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

Open

      def request_publish_approval
        User.with_current_user current_user do
          c = self.controller_name.downcase
          a = self.action_name.downcase

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

Open

  def uploaded_data_with_extension=(file_data)
    unless self.class == ForumAttachment || self.class == HelpAttachment || self.class == HelpImage #FIXME: This check is an indication that this extension is applied too broadly, I think.
      upload_results = self.uploaded_data_without_extension=file_data
      self.original_filename = file_data.original_filename

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

Open

def recursively_set_mime_type(list, depth, type)
  depth -= 1
  list.map do |el|
    if depth == 0
      el == "application/x-error" ? el : type

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Method ontology_select_tag_old has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

        def ontology_select_tag_old form, type, root_id, element_id, selected_id=nil, html_options={}

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

Open

    def extract_from_document doc
      doc.root.namespaces.default_prefix = "ss"


      template_sheet = nil

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

Open

def copy_file_between_zips(src, dest, name, ext)
  if name.ends_with?('.error')
    new_name = name
  else
    new_name = ext.nil? ? name : "#{name}#{ext}"

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

Open

      def cache_remote_content_blob
        blobs = []
        blobs << self.content_blob if self.respond_to?(:content_blob)
        blobs = blobs | self.content_blobs if self.respond_to?(:content_blobs)
        blobs.compact!

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Consider simplifying this complex logical expression.

Open

          unless res.nil?
            permissions.can_view = res["can_view"].to_s==@@expected_true_value && state_allows_manage?(user)
            permissions.can_download = res["can_download"].to_s==@@expected_true_value && state_allows_manage?(user)
            permissions.can_edit = res["can_edit"].to_s==@@expected_true_value && state_allows_manage?(user)
            permissions.can_manage = res["can_manage"].to_s==@@expected_true_value && state_allows_manage?(user)

Function showDataTooltip has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

function showDataTooltip(prefix,pagex,pagey,valuex,valuey) {

Function performSearch has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

  function performSearch(data, regexps, queries, highlighters, state) {

Function select_cells has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

function select_cells(startCol, startRow, endCol, endRow, sheetNumber) {

Method create_job has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def self.create_job subscribable_type, subscribable_id, project_ids, t=5.seconds.from_now, priority=1

Method feedback has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def feedback user,topic,details,send_anonymously,base_host

Method create_job has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def self.create_job subscribable_type, subscribable_id, old_project_ids, t=5.seconds.from_now, priority=1