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

      def cache_path(size=nil, include_local_name=false)
        id = self.kind_of?(Integer) ? self : self.id
        if self.kind_of?(ContentBlob)
          rtn = Seek::Config.temporary_filestore_path + '/image_assets'
        elsif self.kind_of?(Avatar)
Severity: Minor
Found in lib/seek/acts_as_fleximage_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 update_timestamps has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

          def update_timestamps(from, to)
            begin
              ["updated_at"].each do |key|
                if to.has_attribute?(key)
                  logger.debug("explicit_versioning - update_timestamps method - setting timestamp_column '#{key}'")
Severity: Minor
Found in lib/explicit_versioning.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 resolve_admin_defined_role_projects has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def resolve_admin_defined_role_projects
      projects =  Seek::Config.project_hierarchy_enabled ? self.projects_and_descendants : self.projects

      admin_defined_role_projects.each do |role|
        unless projects.include?(role.project)
Severity: Minor
Found in lib/seek/admin_defined_roles.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

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

        def ontology_editor_display type, root_id=nil, selected_id=nil

          # login users can edit new defined assay/technology types
          # only admin can edit/delete new defined assay/technology types
          show_edit = false
Severity: Minor
Found in lib/acts_as_ontology_view_helper.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

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  function cornerHandleMove(newPos, element)
  {
    _width = newPos.X + EDGE_THICKNESS;
    _height = newPos.Y + EDGE_THICKNESS;
    UpdatePositions();
Severity: Minor
Found in app/assets/javascripts/jws/Resizeable_Textbox/javascript.js and 1 other location - About 35 mins to fix
app/assets/javascripts/jws/Resizeable_Container/javascript.js on lines 380..385

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 46.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  function cornerHandleMove(newPos, element)
  {
    _width = newPos.X + EDGE_THICKNESS;
    _height = newPos.Y + EDGE_THICKNESS;
    UpdatePositions2();
Severity: Minor
Found in app/assets/javascripts/jws/Resizeable_Container/javascript.js and 1 other location - About 35 mins to fix
app/assets/javascripts/jws/Resizeable_Textbox/javascript.js on lines 387..392

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 46.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        specimen_data = specimen_titles.
        zip(specimen_sexes, specimen_ages, specimen_age_units,
            specimen_comments, organism_titles, strain_titles, genotype_titles, genotype_modifications).
        map do |specimen_title, specimen_sex, specimen_age, specimen_age_unit,
            specimen_comment, organism_title, strain_title, genotype_title, genotype_modification |
Severity: Minor
Found in lib/seek/data/bio_samples.rb and 1 other location - About 30 mins to fix
lib/seek/data/bio_samples.rb on lines 412..414

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 33.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

          samples_data = sample_titles.zip(sample_types, sample_donation_dates, sample_comments, sample_organism_parts, tissue_and_cell_types, sop_titles, institution_titles, specimen_titles).map do |sample_title, sample_type, sample_donation_date, sample_comment, sample_organism_part, tissue_and_cell_type, sop_title, institution_title, specimen_title|
            {:sample_title => sample_title, :sample_type => sample_type, :sample_donation_date => sample_donation_date, :sample_comment => sample_comment, :sample_organism_part => sample_organism_part,
             :tissue_and_cell_type => tissue_and_cell_type, :sop_title => sop_title, :institution_title => institution_title, :specimen_title => specimen_title}
Severity: Minor
Found in lib/seek/data/bio_samples.rb and 1 other location - About 30 mins to fix
lib/seek/data/bio_samples.rb on lines 377..384

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 33.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Avoid too many return statements within this function.
Open

                return [arcIntersections[0], arcIntersections[1]];
Severity: Major
Found in app/assets/javascripts/modified_cytoscape.js - About 30 mins to fix

    Avoid too many return statements within this method.
    Open

        return nil
    Severity: Major
    Found in app/models/content_blob.rb - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

                      return [arcIntersections[0], arcIntersections[1]];
      Severity: Major
      Found in app/assets/javascripts/modified_cytoscape.js - About 30 mins to fix

        Avoid too many return statements within this function.
        Open

                        return [arcIntersections[0], arcIntersections[1]];
        Severity: Major
        Found in app/assets/javascripts/modified_cytoscape.js - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                          return [arcIntersections[0], arcIntersections[1]];
          Severity: Major
          Found in app/assets/javascripts/modified_cytoscape.js - About 30 mins to fix

            Avoid too many return statements within this method.
            Open

                    return I18n.t('access.managing')
            Severity: Major
            Found in app/models/policy.rb - About 30 mins to fix
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