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app/controllers/biological_associations_controller.rb

Summary

Maintainability
B
4 hrs
Test Coverage

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

  def api_index
    q = ::Queries::BiologicalAssociation::Filter.new(params.merge!(api: true)).all
      .where(project_id: sessions_current_project_id)
      .order('biological_associations.id')
Severity: Minor
Found in app/controllers/biological_associations_controller.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 api_index has 26 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def api_index
    q = ::Queries::BiologicalAssociation::Filter.new(params.merge!(api: true)).all
      .where(project_id: sessions_current_project_id)
      .order('biological_associations.id')
Severity: Minor
Found in app/controllers/biological_associations_controller.rb - About 1 hr to fix

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

        @biological_association.destroy
    Severity: Minor
    Found in app/controllers/biological_associations_controller.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 allow: - update or save calls, assigned to a variable, or used as a condition in an if/unless/case statement. - create calls, assigned to a variable that then has a call to persisted?. - calls if the result is explicitly returned from methods and blocks, or provided as arguments. - calls whose signature doesn't look like an ActiveRecord persistence method.

    By default it will also allow implicit returns from methods and blocks. that behavior can be turned off with AllowImplicitReturn: false.

    You can permit receivers that are giving false positives with AllowedReceivers: []

    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

def save_user
  return user.save
end

    Example: AllowImplicitReturn: true (default)

    # good
users.each { |u| u.save }

def save_user
  user.save
end

    Example: AllowImplicitReturn: false

    # bad
users.each { |u| u.save }
def save_user
  user.save
end

# good
users.each { |u| u.save! }

def save_user
  user.save!
end

def save_user
  return user.save
end

    Example: AllowedReceivers: ['merchant.customers', 'Service::Mailer']

    # bad
merchant.create
customers.builder.save
Mailer.create

module Service::Mailer
  self.create
end

# good
merchant.customers.create
MerchantService.merchant.customers.destroy
Service::Mailer.update(message: 'Message')
::Service::Mailer.update
Services::Service::Mailer.update(message: 'Message')
Service::Mailer::update

    Similar blocks of code found in 22 locations. Consider refactoring.
    Open

      def create
    @biological_association = BiologicalAssociation.new(biological_association_params)
    respond_to do |format|
      if @biological_association.save
        format.html { redirect_to @biological_association, notice: 'Biological association was successfully created.' }
    Severity: Major
    Found in app/controllers/biological_associations_controller.rb and 21 other locations - About 1 hr to fix
    app/controllers/asserted_distributions_controller.rb on lines 43..51
    app/controllers/attributions_controller.rb on lines 42..51
    app/controllers/biological_associations_graphs_controller.rb on lines 44..53
    app/controllers/biological_relationships_controller.rb on lines 61..70
    app/controllers/character_states_controller.rb on lines 29..38
    app/controllers/collection_object_observations_controller.rb on lines 30..40
    app/controllers/collection_profiles_controller.rb on lines 33..42
    app/controllers/common_names_controller.rb on lines 46..55
    app/controllers/dataset_records_controller.rb on lines 28..37
    app/controllers/depictions_controller.rb on lines 71..79
    app/controllers/extracts_controller.rb on lines 44..53
    app/controllers/gene_attributes_controller.rb on lines 33..42
    app/controllers/loans_controller.rb on lines 49..58
    app/controllers/observation_matrices_controller.rb on lines 47..56
    app/controllers/organizations_controller.rb on lines 36..45
    app/controllers/origin_relationships_controller.rb on lines 43..52
    app/controllers/otu_page_layouts_controller.rb on lines 31..40
    app/controllers/protocol_relationships_controller.rb on lines 47..56
    app/controllers/protocols_controller.rb on lines 40..49
    app/controllers/ranged_lot_categories_controller.rb on lines 29..38
    app/controllers/sequences_controller.rb on lines 38..47

    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 47.

    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 23 locations. Consider refactoring.
    Open

      def update
    respond_to do |format|
      if @biological_association.update(biological_association_params)
        format.html { redirect_to @biological_association, notice: 'Biological association was successfully updated.' }
        format.json { render :show, status: :ok, location: @biological_association }
    Severity: Major
    Found in app/controllers/biological_associations_controller.rb and 22 other locations - About 55 mins to fix
    app/controllers/asserted_distributions_controller.rb on lines 58..65
    app/controllers/attributions_controller.rb on lines 58..65
    app/controllers/biological_associations_graphs_controller.rb on lines 60..67
    app/controllers/biological_relationships_controller.rb on lines 77..84
    app/controllers/character_states_controller.rb on lines 45..52
    app/controllers/collection_object_observations_controller.rb on lines 47..55
    app/controllers/common_names_controller.rb on lines 62..69
    app/controllers/confidences_controller.rb on lines 55..62
    app/controllers/depictions_controller.rb on lines 86..93
    app/controllers/documents_controller.rb on lines 45..52
    app/controllers/extracts_controller.rb on lines 60..67
    app/controllers/gene_attributes_controller.rb on lines 49..56
    app/controllers/images_controller.rb on lines 87..94
    app/controllers/observation_matrices_controller.rb on lines 63..70
    app/controllers/organizations_controller.rb on lines 52..59
    app/controllers/origin_relationships_controller.rb on lines 59..66
    app/controllers/otu_page_layouts_controller.rb on lines 47..54
    app/controllers/protocol_relationships_controller.rb on lines 63..70
    app/controllers/protocols_controller.rb on lines 56..63
    app/controllers/ranged_lot_categories_controller.rb on lines 45..52
    app/controllers/sequences_controller.rb on lines 54..61
    app/controllers/type_materials_controller.rb on lines 58..65

    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 44.

    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 5 locations. Consider refactoring.
    Open

      def index
    respond_to do |format|
      format.html {
        @recent_objects = BiologicalAssociation.recent_from_project_id(sessions_current_project_id).order(updated_at: :desc).limit(10)
        render '/shared/data/all/index'
    Severity: Major
    Found in app/controllers/biological_associations_controller.rb and 4 other locations - About 55 mins to fix
    app/controllers/extracts_controller.rb on lines 9..19
    app/controllers/georeferences_controller.rb on lines 8..18
    app/controllers/images_controller.rb on lines 9..18
    app/controllers/observations_controller.rb on lines 9..21

    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 44.

    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 5 locations. Consider refactoring.
    Open

      def batch_update
    if r = BiologicalAssociation.batch_update(
        preview: params[:preview],
        biological_association: biological_association_params.merge(by: sessions_current_user_id),
        biological_association_query: params[:biological_association_query] )
    Severity: Major
    Found in app/controllers/biological_associations_controller.rb and 4 other locations - About 35 mins to fix
    app/controllers/asserted_distributions_controller.rb on lines 117..126
    app/controllers/collecting_events_controller.rb on lines 128..136
    app/controllers/collection_objects_controller.rb on lines 402..410
    app/controllers/otus_controller.rb on lines 254..263

    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

        @biological_associations = ::Queries::BiologicalAssociation::Filter.new(params.merge!(api: true))
      .all
      .where(project_id: sessions_current_project_id)
      .order('biological_associations.id')
      .page(params[:page])
    Severity: Minor
    Found in app/controllers/biological_associations_controller.rb and 1 other location - About 15 mins to fix
    app/controllers/collection_objects_controller.rb on lines 366..369

    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

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