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Method create has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def create
    @help_document = HelpDocument.new(params[:help_document]) 
    if params[:commit] == "Preview"
      @preview = true
    end
Severity: Minor
Found in app/controllers/help_documents_controller.rb - About 25 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 project_or_institution_details has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def project_or_institution_details projects_or_institutions
    details = ''
    unless params[projects_or_institutions].blank?
      params[projects_or_institutions].each do |project_or_institution|
        project_or_institution_details= project_or_institution.split(',')
Severity: Minor
Found in app/controllers/people_controller.rb - About 25 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_version has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def new_version
    if (handle_data nil)
      comments=params[:revision_comment]

      respond_to do |format|
Severity: Minor
Found in app/controllers/workflows_controller.rb - About 25 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_version has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def new_version
    if handle_upload_data
      comments=params[:revision_comment]
Severity: Minor
Found in app/controllers/sops_controller.rb - About 25 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 existing_specimens has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def existing_specimens
    specimens_of_strains = []
    strains = []
    specimens_with_default_strain =[]
    if params[:strain_ids]
Severity: Minor
Found in app/controllers/biosamples_controller.rb - About 25 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 update has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def update

    # extra check required to see if any avatar was actually selected (or it remains to be the default one)
    avatar_id = params[:institution].delete(:avatar_id).to_i
    @institution.avatar_id = ((avatar_id.kind_of?(Numeric) && avatar_id > 0) ? avatar_id : nil)
Severity: Minor
Found in app/controllers/institutions_controller.rb - About 25 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 create has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def create
    @studied_factor=StudiedFactor.new(params[:studied_factor])
    @studied_factor.data_file=@data_file
    @studied_factor.data_file_version = params[:version]
    new_substances = params[:substance_autocompleter_unrecognized_items] || []
Severity: Minor
Found in app/controllers/studied_factors_controller.rb - About 25 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 6 (exceeds 5 allowed). Consider refactoring.
Open

  def destroy
    respond_to do |format|
      if @specimen.destroy
        format.html { redirect_to(specimens_path) }
        format.xml { head :ok }
Severity: Minor
Found in app/controllers/specimens_controller.rb - About 25 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 build_resource_hash has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def build_resource_hash(assets)
      resource_hash={}
      assets.each do |res|
        resource_hash[res.class.name] = {:items => [], :hidden_count => 0} unless resource_hash[res.class.name]
        resource_hash[res.class.name][:items] << res
Severity: Minor
Found in app/controllers/scales_controller.rb - About 25 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 edit has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def edit
    
    possible_unsaved_data = "unsaved_#{@project.class.name}_#{@project.id}".to_sym
    if session[possible_unsaved_data]
      # if user was redirected to this 'edit' page from avatar upload page - use session
Severity: Minor
Found in app/controllers/projects_controller.rb - About 25 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_version has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def new_version
    if handle_upload_data
      comments=params[:revision_comment]

      #@presentation.content_blob = ContentBlob.new(:tmp_io_object => @tmp_io_object, :url=>@data_url)
Severity: Minor
Found in app/controllers/presentations_controller.rb - About 25 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_tools_and_expertise has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def set_tools_and_expertise person,params
      exp_changed = person.tag_with_params params,"expertise"
      tools_changed = person.tag_with_params params,"tool"
      if immediately_clear_tag_cloud?
        expire_annotation_fragments("expertise") if exp_changed
Severity: Minor
Found in app/controllers/people_controller.rb - About 25 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 6 (exceeds 5 allowed). Consider refactoring.
Open

  def new
    @project = Project.new

    possible_unsaved_data = "unsaved_#{@project.class.name}_#{@project.id}".to_sym
    if session[possible_unsaved_data]
Severity: Minor
Found in app/controllers/projects_controller.rb - About 25 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_avatars has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def find_avatars
    # all avatars for current object are only shown to the owner of the object OR to any admin (if the object is not an admin themself);
    # also, show avatars to all members of a project/institution
    if User.admin_logged_in? || (@avatar_owner_instance.class.name == "Person" && @avatar_for_id.to_i == current_user.person.id.to_i) ||
     (["Project", "Institution"].include?(@avatar_for) && @avatar_owner_instance.can_be_edited_by?(current_user))
Severity: Minor
Found in app/controllers/avatars_controller.rb - About 25 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 update has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def update
    update_annotations @strain
    if params[:sharing]
      @strain.policy.set_attributes_with_sharing params[:sharing], @strain.projects
    end
Severity: Minor
Found in app/controllers/strains_controller.rb - About 25 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 auth_params has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def auth_params
    restricted_params={:sharing => User.admin_logged_in?,
                       :site_root_uri => User.admin_logged_in?,
                       :site_username => User.admin_logged_in?,
                       :site_password => User.admin_logged_in?,
Severity: Minor
Found in app/controllers/projects_controller.rb - About 25 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 resolve_tags_from_params has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def resolve_tags_from_params params, attr
      tags=[]

        selected_key = "#{attr}_autocompleter_selected_ids".to_sym
        unrecognized_key = "#{attr}_autocompleter_unrecognized_items".to_sym
Severity: Minor
Found in lib/seek/taggable.rb - About 25 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 start has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def self.start number=0,restart=false
      number = Seek::Config.workflows_enabled ? number : 0

      action = restart ? "restart" : "start"
Severity: Minor
Found in lib/seek/workers.rb - About 25 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 show_via_url has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

      def show_via_url asset, content_blob=nil
        content_blob = content_blob.nil? ? asset.content_blob : content_blob
        code = url_response_code(content_blob.url)
        if (["301","302", "401"].include?(code))
          redirect_to(content_blob.url, :target=>"_blank")
Severity: Minor
Found in lib/seek/download_handling/data_download.rb - About 25 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 included has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

      def self.included klass
        attr_accessor :permission_for
        klass.extend AuthLookupClassMethods
        klass.class_eval do
          belongs_to :contributor, :polymorphic => true unless method_defined? :contributor
Severity: Minor
Found in lib/seek/permissions/policy_based_authorization.rb - About 25 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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