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Method open_id_authentication has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def open_id_authentication
    authenticate_with_open_id do |result, identity_url|
      if result.successful?
        if @user = User.find_by_openid(identity_url)          
          check_login
Severity: Minor
Found in app/controllers/sessions_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method find_ontology_class has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def find_ontology_class
    uri = params[:uri] || Seek::Ontologies::TechnologyTypeReader.instance.default_parent_class_uri.to_s
    cls = Seek::Ontologies::TechnologyTypeReader.instance.class_hierarchy.hash_by_uri[uri]
    cls ||= SuggestedTechnologyType.where(:uri => uri).first
    if cls.nil?
Severity: Minor
Found in app/controllers/technology_types_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method destroy has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def destroy

    respond_to do |format|
      if @assay.can_delete?(current_user) && @assay.destroy
        format.html { redirect_to(assays_url) }
Severity: Minor
Found in app/controllers/assays_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method set_openid has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def set_openid
    @user = User.find(params[:id])
    authenticate_with_open_id do |result, identity_url|
      if result.successful?
        @user.openid = identity_url
Severity: Minor
Found in app/controllers/users_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method assign_protected has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def assign_protected
      @topic.user     = current_user if @topic.new_record?
      # admins and moderators can sticky and lock topics
      return unless admin? or current_user.moderator_of?(@topic.forum)
      @topic.sticky, @topic.locked = params[:topic][:sticky], params[:topic][:locked]
Severity: Minor
Found in app/controllers/topics_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method smtp_settings has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def smtp_settings field
      value = self.smtp[field.to_sym]
      if field == :password || field == 'password'
        if !value.blank?
          begin
Severity: Minor
Found in lib/seek/config.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method process_view_for_successful_url has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

      def process_view_for_successful_url(url)
        headers = fetch_url_headers(url)
        @content_type = headers[:content_type]
        @size = headers[:content_length]
        @size_mb = @size.to_i / 10_000
Severity: Minor
Found in lib/seek/upload_handling/examine_url.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method preprocess_doi_or_pubmed has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def preprocess_doi_or_pubmed pubmed_id,doi
    doi = doi.sub(%r{doi\.*:}i,"").strip unless doi.nil?
    doi.strip! unless doi.nil?
    pubmed_id.strip! unless pubmed_id.nil? || pubmed_id.is_a?(Fixnum)
    return pubmed_id,doi
Severity: Minor
Found in app/controllers/publications_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method new has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def new
    @study = Study.new
    @study.create_from_asset = params[:create_from_asset]
    @study.new_link_from_assay = params[:new_link_from_assay]
    investigation = nil
Severity: Minor
Found in app/controllers/studies_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method destroy has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def destroy
      if @run.destroy
        flash[:notice] = "Run was deleted."
        respond_with(@run) do |format|
          format.html { redirect_to params[:redirect_to].blank? ? :back : params[:redirect_to]}
Severity: Minor
Found in app/controllers/taverna_player/runs_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method determine_filename_from_url has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

      def determine_filename_from_url(url)
        filename = nil
        if valid_uri?(url)
          path = URI.parse(url).path
          filename = path.split('/').last unless path.nil?
Severity: Minor
Found in lib/seek/upload_handling/content_inspection.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method classify_for_tabs has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def classify_for_tabs result_collection
      results={}

      result_collection.each do |res|
        tab = res.respond_to?(:tab) ? res.tab : res.class.name
Severity: Minor
Found in lib/seek/faceted_browsing.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method check_allowed_to_manage_types has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def check_allowed_to_manage_types
    unless Seek::Config.type_managers_enabled
      error("Type management disabled", "...")
      return false
    end
Severity: Minor
Found in app/controllers/application_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method published_date has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

      def published_date
        published_date = nil
        #first parse published date on PHST - Publication History Status Date
        history_status_date = @pubmed['PHST']
        unless history_status_date.blank?
Severity: Minor
Found in lib/seek/bio_extension.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method last_asset_id_for_user has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

        def last_asset_id_for_user user_id
          unless user_id.is_a?(Numeric)
            user_id = user_id.nil? ? 0 : user_id.id
          end
          v = ActiveRecord::Base.connection.select_one("select max(asset_id) from #{lookup_table_name} where user_id = #{user_id}").values[0]
Severity: Minor
Found in lib/seek/permissions/policy_based_authorization.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method authorize_asset_collection has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

        def authorize_asset_collection assets, action, user=User.current_user,filter_by_permissions=true
          return assets if assets.empty?
          user_id = user.nil? ? 0 : user.id
          if Seek::Config.auth_lookup_enabled && self.lookup_table_consistent?(user_id)
            ids=assets.collect{|asset| asset.id}
Severity: Minor
Found in lib/seek/permissions/policy_based_authorization.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method download_via_url has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def download_via_url
      code = url_response_code(@content_blob.url)
      if code == "200"
        downloader=Seek::RemoteDownloader.new
        begin
Severity: Minor
Found in lib/seek/content_blob_common.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method format_csv has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

def format_csv(output, index = [])
  row_limit = 500
  html = ''

  begin
Severity: Minor
Found in lib/taverna_player_renderers.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method initialize has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

      def initialize xml=nil
        @sample_names = []
        @values = {}
        unless xml.nil?
          begin
Severity: Minor
Found in lib/seek/data/treatments.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method index has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def index
    controller = self.controller_name.downcase
    unless Seek::Config.faceted_browsing_enabled && Seek::Config.facet_enable_for_pages[controller] && ie_support_faceted_browsing?
      model_name=controller.classify
      model_class=eval(model_name)
Severity: Minor
Found in lib/index_pager.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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