Sign upLogin

SpeciesFileGroup/taxonworks

View on GitHub
Star
app/models/sequence.rb

Summary

Maintainability
A
2 hrs
Test Coverage

Method has too many lines. [39/25]
Open

  def self.used_recently(user_id, project_id, used_on = nil)
    return Sequence.none if used_on.nil?
    t = case used_on
        when 'GeneAttribute'
          GeneAttribute.arel_table
Severity: Minor
Found in app/models/sequence.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 used_recently has 39 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def self.used_recently(user_id, project_id, used_on = nil)
    return Sequence.none if used_on.nil?
    t = case used_on
        when 'GeneAttribute'
          GeneAttribute.arel_table
Severity: Minor
Found in app/models/sequence.rb - About 1 hr to fix

    Prefer 1.week.
    Open

          .where(t['updated_at'].gt( 1.weeks.ago ))
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop checks for correct grammar when using ActiveSupport's core extensions to the numeric classes.

    Example:

    # bad
3.day.ago
1.months.ago

# good
3.days.ago
1.month.ago

    Prefer 1.week.
    Open

                  t['updated_at'].gt(1.weeks.ago)
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop checks for correct grammar when using ActiveSupport's core extensions to the numeric classes.

    Example:

    # bad
3.day.ago
1.months.ago

# good
3.days.ago
1.month.ago

    Specify a :dependent option.
    Open

      has_many :gene_attributes, inverse_of: :sequence
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop looks for has_many or has_one associations that don't specify a :dependent option. It doesn't register an offense if :through option was specified.

    Example:

    # bad
class User < ActiveRecord::Base
  has_many :comments
  has_one :avatar
end

# good
class User < ActiveRecord::Base
  has_many :comments, dependent: :restrict_with_exception
  has_one :avatar, dependent: :destroy
  has_many :patients, through: :appointments
end

    Specify a :dependent option.
    Open

        has_many relationships, class_name: d.name.to_s, foreign_key: :object_sequence_id, inverse_of: :object_sequence
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop looks for has_many or has_one associations that don't specify a :dependent option. It doesn't register an offense if :through option was specified.

    Example:

    # bad
class User < ActiveRecord::Base
  has_many :comments
  has_one :avatar
end

# good
class User < ActiveRecord::Base
  has_many :comments, dependent: :restrict_with_exception
  has_one :avatar, dependent: :destroy
  has_many :patients, through: :appointments
end

    Use a string value for class_name.
    Open

        has_many relationships, class_name: d.name.to_s, foreign_key: :object_sequence_id, inverse_of: :object_sequence
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop checks if the value of the option class_name, in the definition of a reflection is a string.

    Example:

    # bad
has_many :accounts, class_name: Account
has_many :accounts, class_name: Account.name

# good
has_many :accounts, class_name: 'Account'

    Specify a :dependent option.
    Open

      has_many :sequence_relationships, foreign_key: :subject_sequence_id, inverse_of: :subject_sequence # this sequence describes others
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop looks for has_many or has_one associations that don't specify a :dependent option. It doesn't register an offense if :through option was specified.

    Example:

    # bad
class User < ActiveRecord::Base
  has_many :comments
  has_one :avatar
end

# good
class User < ActiveRecord::Base
  has_many :comments, dependent: :restrict_with_exception
  has_one :avatar, dependent: :destroy
  has_many :patients, through: :appointments
end

    Prefer 1.week.
    Open

                .where(t['updated_at'].gt( 1.weeks.ago ))
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop checks for correct grammar when using ActiveSupport's core extensions to the numeric classes.

    Example:

    # bad
3.day.ago
1.months.ago

# good
3.days.ago
1.month.ago

    Specify a :dependent option.
    Open

      has_many :related_sequence_relationships, class_name: 'SequenceRelationship', foreign_key: :object_sequence_id, inverse_of: :object_sequence # attributes of this sequence
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop looks for has_many or has_one associations that don't specify a :dependent option. It doesn't register an offense if :through option was specified.

    Example:

    # bad
class User < ActiveRecord::Base
  has_many :comments
  has_one :avatar
end

# good
class User < ActiveRecord::Base
  has_many :comments, dependent: :restrict_with_exception
  has_one :avatar, dependent: :destroy
  has_many :patients, through: :appointments
end

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

              t.project(t['object_sequence_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.weeks.ago)
            )
              .where(t['created_by_id'].eq(user_id))
    Severity: Minor
    Found in app/models/sequence.rb and 1 other location - About 35 mins to fix
    app/models/sequence.rb on lines 105..109

    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 34.

    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

              t.project(t['sequence_id'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.weeks.ago ))
            .where(t['created_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'])
    Severity: Minor
    Found in app/models/sequence.rb and 1 other location - About 35 mins to fix
    app/models/sequence.rb on lines 97..103

    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 34.

    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 the new style validations validates :column, inclusion: value over validates_inclusion_of.
    Open

      validates_inclusion_of :sequence_type, in: ['DNA', 'RNA', 'AA']
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop checks for the use of old-style attribute validation macros.

    Example:

    # bad
validates_acceptance_of :foo
validates_confirmation_of :foo
validates_exclusion_of :foo
validates_format_of :foo
validates_inclusion_of :foo
validates_length_of :foo
validates_numericality_of :foo
validates_presence_of :foo
validates_absence_of :foo
validates_size_of :foo
validates_uniqueness_of :foo

# good
validates :foo, acceptance: true
validates :foo, confirmation: true
validates :foo, exclusion: true
validates :foo, format: true
validates :foo, inclusion: true
validates :foo, length: true
validates :foo, numericality: true
validates :foo, presence: true
validates :foo, absence: true
validates :foo, size: true
validates :foo, uniqueness: true

    Prefer the new style validations validates :column, presence: value over validates_presence_of.
    Open

      validates_presence_of :sequence
    Severity: Minor
    Found in app/models/sequence.rb by rubocop

    This cop checks for the use of old-style attribute validation macros.

    Example:

    # bad
validates_acceptance_of :foo
validates_confirmation_of :foo
validates_exclusion_of :foo
validates_format_of :foo
validates_inclusion_of :foo
validates_length_of :foo
validates_numericality_of :foo
validates_presence_of :foo
validates_absence_of :foo
validates_size_of :foo
validates_uniqueness_of :foo

# good
validates :foo, acceptance: true
validates :foo, confirmation: true
validates :foo, exclusion: true
validates :foo, format: true
validates :foo, inclusion: true
validates :foo, length: true
validates :foo, numericality: true
validates :foo, presence: true
validates :foo, absence: true
validates :foo, size: true
validates :foo, uniqueness: true

    There are no issues that match your filters.

    Category
    Status