SysMO-DB/seek

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Method create has a Cognitive Complexity of 35 (exceeds 5 allowed). Consider refactoring.
Open

  def create
    @sample = Sample.new(params[:sample])
    # create new specimen only for combined form
    is_new_spec = params[:sample][:specimen_id].nil? ? true : false

Severity: Minor
Found in app/controllers/samples_controller.rb - About 5 hrs 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 is_authorized? has a Cognitive Complexity of 35 (exceeds 5 allowed). Consider refactoring.
Open

      def self.is_authorized?(action, thing_type, thing, user=nil)

        # initially not authorized, so if all tests fail -
        # safe result of being not authorized will get returned
        is_authorized = false
Severity: Minor
Found in lib/seek/permissions/authorization.rb - About 5 hrs 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 populate_sample has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.
Open

    def populate_sample sample_json, specimen, assay=nil


        sample_title = sample_json["title"]
        sample_type = sample_json["type"]
Severity: Minor
Found in lib/seek/data/bio_samples.rb - About 5 hrs 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 dortmund_hengstler_mapping has 123 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def dortmund_hengstler_mapping

      age_regex = /(\d+-?\d*)\s*(day|week|month|year)s?/i
      treatment_regex = /(\d*\.?\d*)\s*(\w+\/\w+)\s*([\w\.\s,']*),?\s+([\w\.]*)/
      incubation_time_regex = /(\d+\.?\d*)(\w{1})/
Severity: Major
Found in lib/seek/parser_mapper.rb - About 4 hrs to fix

    File person.rb has 366 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    require 'grouped_pagination'
    
    class Person < ActiveRecord::Base
    
      include Seek::Rdf::RdfGeneration
    Severity: Minor
    Found in app/models/person.rb - About 4 hrs to fix

      Method included has a Cognitive Complexity of 32 (exceeds 5 allowed). Consider refactoring.
      Open

            def self.included klass
              klass.class_eval do
                include Seek::Search::CommonFields
      
                searchable do
      Severity: Minor
      Found in lib/seek/search/search_sunspot.rb - About 4 hrs 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_default_subscriptions has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
      Open

        def set_default_subscriptions projects
          unless projects.empty?
            Person.scoped(:include => :project_subscriptions).each do |person|
              project_subscriptions = person.project_subscriptions
              project_subscriptions.each do |ps|
      Severity: Minor
      Found in lib/subscribable.rb - About 4 hrs 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

      File people_controller.rb has 357 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      class PeopleController < ApplicationController
      
        include Seek::AnnotationCommon
        include Seek::Publishing::PublishingCommon
        include Seek::Publishing::GatekeeperPublish
      Severity: Minor
      Found in app/controllers/people_controller.rb - About 4 hrs to fix

        Method submit_to_jws has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.
        Open

          def submit_to_jws
            following_action=params.delete("following_action")
            error=nil
        
            #FIXME: currently we have to assume that a model with multiple files only contains 1 model file that would be executed on jws online, and only the first one is chosen
        Severity: Minor
        Found in app/controllers/models_controller.rb - About 4 hrs 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

        Class Policy has 34 methods (exceeds 20 allowed). Consider refactoring.
        Open

        class Policy < ActiveRecord::Base
          
          has_many :permissions,
                   :dependent => :destroy,
                   :order => "created_at ASC",
        Severity: Minor
        Found in app/models/policy.rb - About 4 hrs to fix

          Method list_samples_and_assay_organisms has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.
          Open

            def list_samples_and_assay_organisms attribute, assay_samples, assay_organisms, html_options={}, none_text="Not Specified"
          
              result= "<p class='#{html_options[:class]}' id='#{html_options[:id]}'> <b>#{attribute}</b>: "
          
              result +="<span class='none_text'>#{none_text}</span>" if assay_samples.blank? and assay_organisms.blank?
          Severity: Minor
          Found in app/helpers/assays_helper.rb - About 4 hrs 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 perform_search has a Cognitive Complexity of 29 (exceeds 5 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]
          Severity: Minor
          Found in app/controllers/search_controller.rb - About 4 hrs 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

          Class ApplicationController has 33 methods (exceeds 20 allowed). Consider refactoring.
          Open

          class ApplicationController < ActionController::Base
          
            include Seek::Errors::ControllerErrorHandling
            include Seek::EnabledFeaturesFilter
            include Recaptcha::Verify
          Severity: Minor
          Found in app/controllers/application_controller.rb - About 4 hrs to fix

            Class BioSamples has 33 methods (exceeds 20 allowed). Consider refactoring.
            Open

                class BioSamples
            
                attr_reader :investigation, :study, :assay, :assay_class, :assay_type,
                            :units, :treatments, :organisms, :strains, :culture_growth_type, :tissue_and_cell_types,
                            :specimens, :samples,  :specimen_names, :sample_names, :treatments,:treatments_text,
            Severity: Minor
            Found in lib/seek/data/bio_samples.rb - About 4 hrs to fix

              Method create_or_update_attributions has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.
              Open

                def self.create_or_update_attributions(resource, attributions_from_params, predicate = Relationship::ATTRIBUTED_TO)
              
                  # added this branching on .nil? because of the danger of loosing all attributions for a model (for example) if due to an incomplete post request attributions is nil
                  # the former code interpreted a nil parameter as an empty list => remove all attributions from an asset
                  unless attributions_from_params.nil?
              Severity: Minor
              Found in app/models/relationship.rb - About 4 hrs 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 dortmund_bcat_ko_mapping has 102 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  def dortmund_bcat_ko_mapping
              
                    age_regex = /(\d+-?\d*)\s*(day|week|month|year)s?/i
                    treatment_substance_regex = /.*\((control|treated)\s?=\s?(.*)\)/i
                    treatment_concentration_unit_regex = /(\d*[,\.]?\d*)\s*([\w\s\/]*).*$/
              Severity: Major
              Found in lib/seek/parser_mapper.rb - About 4 hrs to fix

                Function dragObject has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
                Open

                function dragObject(element, attachElement, lowerBound, upperBound, startCallback, moveCallback, endCallback, attachLater)
                {
                  if(typeof(element) == "string")
                    element = document.getElementById(element);
                  if(element == null)
                Severity: Minor
                Found in app/assets/javascripts/jws/Resizeable_Textbox/javascript.js - About 3 hrs 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

                Function dragObject has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
                Open

                function dragObject(element, attachElement, lowerBound, upperBound, startCallback, moveCallback, endCallback, attachLater)
                {
                  if(typeof(element) == "string")
                    element = document.getElementById(element);
                  if(element == null)
                Severity: Minor
                Found in app/assets/javascripts/jws/Resizeable_Container/javascript.js - About 3 hrs 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 27 (exceeds 5 allowed). Consider refactoring.
                Open

                  def update
                    group_name = white_list(params[:favourite_group_name])
                    found = FavouriteGroup.where(:name => group_name, :user_id => current_user.id).first
                    
                    # if the found group with the same is the current one - that's fine; otherwise - can't rename a group with such new name 
                Severity: Minor
                Found in app/controllers/favourite_groups_controller.rb - About 3 hrs 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 27 (exceeds 5 allowed). Consider refactoring.
                Open

                      def self.included klass
                        klass.class_eval do
                          searchable do
                            text :title do
                              if self.respond_to?(:title)
                Severity: Minor
                Found in lib/seek/search/search_sunspot.rb - About 3 hrs 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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