SpeciesFileGroup/taxonworks

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app/models/taxon_name.rb

Summary

Maintainability
F
1 wk
Test Coverage

Class TaxonName has 133 methods (exceeds 20 allowed). Consider refactoring.
Open

class TaxonName < ApplicationRecord

  has_closure_tree

  include Housekeeping
Severity: Major
Found in app/models/taxon_name.rb - About 2 days to fix

    File taxon_name.rb has 977 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    require_dependency Rails.root.to_s + '/app/models/taxon_name_classification.rb'
    require_dependency Rails.root.to_s + '/app/models/taxon_name_relationship.rb'
    
    # A taxonomic name (nomenclature only). See also NOMEN.
    #
    Severity: Major
    Found in app/models/taxon_name.rb - About 2 days to fix

      Method iczn_author_and_year has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring.
      Open

        def iczn_author_and_year
          ay = nil
          p = nil
      
          misapplication = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_string('TaxonNameRelationship::Iczn::Invalidating::Misapplication')
      Severity: Minor
      Found in app/models/taxon_name.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 has too many lines. [46/25]
      Open

        def iczn_author_and_year
          ay = nil
          p = nil
      
          misapplication = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_string('TaxonNameRelationship::Iczn::Invalidating::Misapplication')
      Severity: Minor
      Found in app/models/taxon_name.rb by rubocop

      This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

      Method sv_validate_name has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
      Open

        def sv_validate_name
          correct_name_format = false
      
          if rank_class
            # TODO: name these Regexp somewhere
      Severity: Minor
      Found in app/models/taxon_name.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 sv_missing_original_publication has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
      Open

        def sv_missing_original_publication
          if !self.cached_misspelling && !self.name_is_misapplied?
            if self.source.nil?
              soft_validations.add(:base, 'Original publication is not selected')
            elsif self.origin_citation.pages.blank?
      Severity: Minor
      Found in app/models/taxon_name.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 nomenclature_date has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
      Open

        def nomenclature_date
          return nil if self.id.nil?
           family_before_1961 = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_string('TaxonNameRelationship::Iczn::PotentiallyValidating::FamilyBefore1961').first
      
          # family_before_1961 = taxon_name_relationships.with_type_string('TaxonNameRelationship::Iczn::PotentiallyValidating::FamilyBefore1961').first
      Severity: Minor
      Found in app/models/taxon_name.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

      Consider simplifying this complex logical expression.
      Open

            if (name =~ /^[a-zA-Z]*$/) || # !! should reference NOT_LATIN
                (nomenclatural_code == :iczn && name =~ /^[a-zA-Z]-[a-zA-Z]*$/) ||
                (nomenclatural_code == :icnp && name =~ /^[a-zA-Z]-[a-zA-Z]*$/) ||
                (nomenclatural_code == :icn && name =~  /^[a-zA-Z]*-[a-zA-Z]*$/) ||
                (nomenclatural_code == :icn && name =~  /^[a-zA-Z]*\s×\s[a-zA-Z]*$/) ||
      Severity: Critical
      Found in app/models/taxon_name.rb - About 2 hrs to fix

        Method list_of_invalid_taxon_names has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
        Open

          def list_of_invalid_taxon_names
            first_pass = true
            list = {}
            while first_pass || !list.keys.select{|t| list[t] == false}.empty? do
              first_pass = false
        Severity: Minor
        Found in app/models/taxon_name.rb - About 2 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 icn_author_and_year has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
        Open

          def icn_author_and_year
            ay = nil
        
            basionym = TaxonNameRelationship.where_object_is_taxon_name(self).
              with_type_string('TaxonNameRelationship::Icn::Unaccepting::Usage::Basionym')
        Severity: Minor
        Found in app/models/taxon_name.rb - About 2 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 iczn_author_and_year has 46 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          def iczn_author_and_year
            ay = nil
            p = nil
        
            misapplication = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_string('TaxonNameRelationship::Iczn::Invalidating::Misapplication')
        Severity: Minor
        Found in app/models/taxon_name.rb - About 1 hr to fix

          Method has too many lines. [26/25]
          Open

            def sv_validate_name
              correct_name_format = false
          
              if rank_class
                # TODO: name these Regexp somewhere
          Severity: Minor
          Found in app/models/taxon_name.rb by rubocop

          This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

          Method full_name_hash has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
          Open

            def full_name_hash
              gender = nil
              data   = {}
              safe_self_and_ancestors.each do |i| # !! You can not use self.self_and_ancestors because (this) record is not saved off.
                rank   = i.rank
          Severity: Minor
          Found in app/models/taxon_name.rb - About 1 hr 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 sv_fix_parent_is_valid_name has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
          Open

            def sv_fix_parent_is_valid_name
              if self.parent.unavailable_or_invalid?
                new_parent = self.parent.get_valid_taxon_name
                if self.parent != new_parent
                  self.parent = new_parent
          Severity: Minor
          Found in app/models/taxon_name.rb - About 1 hr 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 sv_validate_name has 26 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

            def sv_validate_name
              correct_name_format = false
          
              if rank_class
                # TODO: name these Regexp somewhere
          Severity: Minor
          Found in app/models/taxon_name.rb - About 1 hr to fix

            Method create_new_combination_if_absent has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
            Open

              def create_new_combination_if_absent
                return true unless type == 'Protonym'
                if !TaxonName.with_cached_html(cached_html).count == 0
                  begin
                    TaxonName.transaction do
            Severity: Minor
            Found in app/models/taxon_name.rb - About 55 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_new_parent_class has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
            Open

              def check_new_parent_class
                if is_protonym? && parent_id != parent_id_was && !parent_id_was.nil? && nomenclatural_code == :iczn
                  if old_parent = TaxonName.find_by(id: parent_id_was)
                    if (rank_name == 'subgenus' || rank_name == 'subspecies') && old_parent.name == name
                      errors.add(:parent_id, "The nominotypical #{rank_name} #{name} can not be moved out of the nominal #{old_parent.rank_name}")
            Severity: Minor
            Found in app/models/taxon_name.rb - About 55 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 get_full_name has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
            Open

              def get_full_name
                return verbatim_name if type != 'Combination' && !GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string) && !verbatim_name.nil?
                return name if type != 'Combination' && !GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string)
                return name if rank_class =~ /Ictv/
                return verbatim_name if !verbatim_name.nil? && type == 'Combination'
            Severity: Minor
            Found in app/models/taxon_name.rb - About 55 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

            Consider simplifying this complex logical expression.
            Open

                if data['species'].nil? && (!data['subspecies'].nil? || !data['variety'].nil? || !data['subvariety'].nil? || !data['form'].nil? || !data['subform'].nil?)
                  data['species'] = [nil, '[SPECIES NOT SPECIFIED]']
                end
            Severity: Major
            Found in app/models/taxon_name.rb - About 40 mins to fix

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

                def sv_fix_missing_author
                  if self.source
                    unless self.source.author.blank?
                      self.verbatim_author = self.source.authority_name
                      begin
              Severity: Minor
              Found in app/models/taxon_name.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 sv_incomplete_combination has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

                def sv_incomplete_combination
                  soft_validations.add(:base, 'The genus in the combination is not specified') if !cached.nil? && cached.include?('GENUS NOT SPECIFIED')
                  soft_validations.add(:base, 'The species in the combination is not specified') if !cached.nil? && cached.include?('SPECIES NOT SPECIFIED')
                  soft_validations.add(:base, 'The variety in the combination is not specified') if !cached.nil? && cached.include?('VARIETY NOT SPECIFIED')
                  soft_validations.add(:base, 'The form in the combination is not specified') if !cached.nil? && cached.include?('FORM NOT SPECIFIED')
              Severity: Minor
              Found in app/models/taxon_name.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 get_full_name_html has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
              Open

                def get_full_name_html(name = nil)
                  name = get_full_name if name.nil? 
                  return name unless is_italicized?
                  n = name 
                  # n = verbatim_name.blank? ? name : verbatim_name
              Severity: Minor
              Found in app/models/taxon_name.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 sv_fix_missing_year has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
              Open

                def sv_fix_missing_year
                  if self.source
                    if self.source.year
                      self.year_of_publication = self.source.year
                      begin
              Severity: Minor
              Found in app/models/taxon_name.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 check_new_rank_class has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
              Open

                def check_new_rank_class
                  # rank_class_was is a AR macro
              
                  if (rank_class != rank_class_was) && !rank_class_was.nil?
              
              
              Severity: Minor
              Found in app/models/taxon_name.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 validate_parent_rank_is_higher has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
              Open

                def validate_parent_rank_is_higher
                  if parent && !rank_class.blank? && rank_string != 'NomenclaturalRank'
                    if RANKS.index(rank_string) <= RANKS.index(parent.rank_string)
                      errors.add(:parent_id, "The parent rank (#{parent.rank_class.rank_name}) is not higher than the rank (#{rank_name}) of this taxon")
                    end
              Severity: Minor
              Found in app/models/taxon_name.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

              Avoid more than 4 levels of block nesting.
              Open

                        ay = '(' + ay + ')' unless ay.empty? if og.name != cg.name
              Severity: Minor
              Found in app/models/taxon_name.rb by rubocop

              This cop checks for excessive nesting of conditional and looping constructs.

              You can configure if blocks are considered using the CountBlocks option. When set to false (the default) blocks are not counted towards the nesting level. Set to true to count blocks as well.

              The maximum level of nesting allowed is configurable.

              Use save! instead of save if the return value is not checked.
              Open

                      self.save
              Severity: Minor
              Found in app/models/taxon_name.rb by rubocop

              This cop identifies possible cases where Active Record save! or related should be used instead of save because the model might have failed to save and an exception is better than unhandled failure.

              This will ignore calls that return a boolean for success if the result is assigned to a variable or used as the condition in an if/unless statement. It will also ignore calls that return a model assigned to a variable that has a call to persisted?. Finally, it will ignore any call with more than 2 arguments as that is likely not an Active Record call or a Model.update(id, attributes) call.

              Example:

              # bad
              user.save
              user.update(name: 'Joe')
              user.find_or_create_by(name: 'Joe')
              user.destroy
              
              # good
              unless user.save
                # ...
              end
              user.save!
              user.update!(name: 'Joe')
              user.find_or_create_by!(name: 'Joe')
              user.destroy!
              
              user = User.find_or_create_by(name: 'Joe')
              unless user.persisted?
                # ...
              end

              Use save! instead of save if the return value is not checked.
              Open

                          self.save
              Severity: Minor
              Found in app/models/taxon_name.rb by rubocop

              This cop identifies possible cases where Active Record save! or related should be used instead of save because the model might have failed to save and an exception is better than unhandled failure.

              This will ignore calls that return a boolean for success if the result is assigned to a variable or used as the condition in an if/unless statement. It will also ignore calls that return a model assigned to a variable that has a call to persisted?. Finally, it will ignore any call with more than 2 arguments as that is likely not an Active Record call or a Model.update(id, attributes) call.

              Example:

              # bad
              user.save
              user.update(name: 'Joe')
              user.find_or_create_by(name: 'Joe')
              user.destroy
              
              # good
              unless user.save
                # ...
              end
              user.save!
              user.update!(name: 'Joe')
              user.find_or_create_by!(name: 'Joe')
              user.destroy!
              
              user = User.find_or_create_by(name: 'Joe')
              unless user.persisted?
                # ...
              end

              Use save! instead of save if the return value is not checked.
              Open

                          self.save
              Severity: Minor
              Found in app/models/taxon_name.rb by rubocop

              This cop identifies possible cases where Active Record save! or related should be used instead of save because the model might have failed to save and an exception is better than unhandled failure.

              This will ignore calls that return a boolean for success if the result is assigned to a variable or used as the condition in an if/unless statement. It will also ignore calls that return a model assigned to a variable that has a call to persisted?. Finally, it will ignore any call with more than 2 arguments as that is likely not an Active Record call or a Model.update(id, attributes) call.

              Example:

              # bad
              user.save
              user.update(name: 'Joe')
              user.find_or_create_by(name: 'Joe')
              user.destroy
              
              # good
              unless user.save
                # ...
              end
              user.save!
              user.update!(name: 'Joe')
              user.find_or_create_by!(name: 'Joe')
              user.destroy!
              
              user = User.find_or_create_by(name: 'Joe')
              unless user.persisted?
                # ...
              end

              Use save! instead of save if the return value is not checked.
              Open

                          self.save
              Severity: Minor
              Found in app/models/taxon_name.rb by rubocop

              This cop identifies possible cases where Active Record save! or related should be used instead of save because the model might have failed to save and an exception is better than unhandled failure.

              This will ignore calls that return a boolean for success if the result is assigned to a variable or used as the condition in an if/unless statement. It will also ignore calls that return a model assigned to a variable that has a call to persisted?. Finally, it will ignore any call with more than 2 arguments as that is likely not an Active Record call or a Model.update(id, attributes) call.

              Example:

              # bad
              user.save
              user.update(name: 'Joe')
              user.find_or_create_by(name: 'Joe')
              user.destroy
              
              # good
              unless user.save
                # ...
              end
              user.save!
              user.update!(name: 'Joe')
              user.find_or_create_by!(name: 'Joe')
              user.destroy!
              
              user = User.find_or_create_by(name: 'Joe')
              unless user.persisted?
                # ...
              end

              TODO found
              Open

                #    TODO: does this form of the name contain parens for subgenus?
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                # return [String, nil, false] # TODO: fix
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                #    TODO: on third thought- eliminate this mess
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                    # TODO: name these Regexp somewhere
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                #    TODO: provide a default to gender (but do NOT eliminate param)
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                # TODO: deprecate all of these for where()
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                # TODO: move to Protonym when we eliminate TaxonName.new()
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                # TODO: move some of these down to Protonym when they don't apply to Combination
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                # TODO: think of a different name, and test
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                # TODO: Can't we just use #valid_id now?
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

              TODO found
              Open

                # TODO: does this make sense now, with #valid_taxon_name_id in place?
              Severity: Minor
              Found in app/models/taxon_name.rb by fixme

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

                def check_new_parent_class
                  if is_protonym? && parent_id != parent_id_was && !parent_id_was.nil? && nomenclatural_code == :iczn
                    if old_parent = TaxonName.find_by(id: parent_id_was)
                      if (rank_name == 'subgenus' || rank_name == 'subspecies') && old_parent.name == name
                        errors.add(:parent_id, "The nominotypical #{rank_name} #{name} can not be moved out of the nominal #{old_parent.rank_name}")
              Severity: Major
              Found in app/models/taxon_name.rb and 1 other location - About 1 hr to fix
              app/models/protonym.rb on lines 682..689

              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 49.

              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

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

                  if data['species'].nil? && (!data['subspecies'].nil? || !data['variety'].nil? || !data['subvariety'].nil? || !data['form'].nil? || !data['subform'].nil?)
                    data['species'] = [nil, '[SPECIES NOT SPECIFIED]']
                  end
              Severity: Minor
              Found in app/models/taxon_name.rb and 1 other location - About 45 mins to fix
              app/models/combination.rb on lines 250..252

              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 41.

              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

                scope :ancestors_and_descendants_of, -> (taxon_name) do
                  a = TaxonName.self_and_ancestors_of(taxon_name)
                  b = TaxonName.descendants_of(taxon_name)
                  TaxonName.from("((#{a.to_sql}) UNION (#{b.to_sql})) as taxon_names")
                end
              Severity: Minor
              Found in app/models/taxon_name.rb and 1 other location - About 15 mins to fix
              app/models/geographic_area.rb on lines 96..100

              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 25.

              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

              Prefer single-quoted strings when you don't need string interpolation or special symbols.
              Open

                    errors.add(:project_id, "The parent taxon is not from the same project") if project_id != parent.project_id
              Severity: Minor
              Found in app/models/taxon_name.rb by rubocop

              Checks if uses of quotes match the configured preference.

              Example: EnforcedStyle: single_quotes (default)

              # bad
              "No special symbols"
              "No string interpolation"
              "Just text"
              
              # good
              'No special symbols'
              'No string interpolation'
              'Just text'
              "Wait! What's #{this}!"

              Example: EnforcedStyle: double_quotes

              # bad
              'Just some text'
              'No special chars or interpolation'
              
              # good
              "Just some text"
              "No special chars or interpolation"
              "Every string in #{project} uses double_quotes"

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