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app/controllers/otus_controller.rb

Summary

Maintainability
D
2 days
Test Coverage

Possible unprotected redirect
Open

        format.html { redirect_to @otu, notice: 'Otu was successfully updated.' }
Severity: Minor
Found in app/controllers/otus_controller.rb by brakeman

Unvalidated redirects and forwards are #10 on the OWASP Top Ten.

Redirects which rely on user-supplied values can be used to "spoof" websites or hide malicious links in otherwise harmless-looking URLs. They can also allow access to restricted areas of a site if the destination is not validated.

Brakeman will raise warnings whenever redirect_to appears to be used with a user-supplied value that may allow them to change the :host option.

For example,

redirect_to params.merge(:action => :home)

will create a warning like

Possible unprotected redirect near line 46: redirect_to(params)

This is because params could contain :host => 'evilsite.com' which would redirect away from your site and to a malicious site.

If the first argument to redirect_to is a hash, then adding :only_path => true will limit the redirect to the current host. Another option is to specify the host explicitly.

redirect_to params.merge(:only_path => true)

redirect_to params.merge(:host => 'myhost.com')

If the first argument is a string, then it is possible to parse the string and extract the path:

redirect_to URI.parse(some_url).path

If the URL does not contain a protocol (e.g., http://), then you will probably get unexpected results, as redirect_to will prepend the current host name and a protocol.

Class OtusController has 42 methods (exceeds 20 allowed). Consider refactoring.
Open

class OtusController < ApplicationController
  include DataControllerConfiguration::ProjectDataControllerConfiguration

  before_action :set_otu, only: [
    :show, :edit, :update, :destroy, :collection_objects, :navigation,
Severity: Minor
Found in app/controllers/otus_controller.rb - About 5 hrs to fix

    File otus_controller.rb has 331 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    class OtusController < ApplicationController
  include DataControllerConfiguration::ProjectDataControllerConfiguration

  before_action :set_otu, only: [
    :show, :edit, :update, :destroy, :collection_objects, :navigation,
    Severity: Minor
    Found in app/controllers/otus_controller.rb - About 3 hrs to fix

      Method create_data_attributes_batch_load has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
      Open

        def create_data_attributes_batch_load
    if params[:file] && digested_cookie_exists?(params[:file].tempfile, :data_attributes_batch_load_otus_md5)
      @result = BatchLoad::Import::Otus::DataAttributesInterpreter.new(**batch_params)
      if @result.create
        flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} TODO RECORD TYPES were created."
      Severity: Minor
      Found in app/controllers/otus_controller.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 distribution has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
      Open

        def distribution
    respond_to do |format|
      format.json do
        @cached_map_type = params[:cached_map_type] || 'CachedMapItem::WebLevel1'
        @quicker_cached_map = @otu.quicker_cached_map(@cached_map_type)
      Severity: Minor
      Found in app/controllers/otus_controller.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

      create returns a model which is always truthy.
      Open

            if @result.create
      Severity: Minor
      Found in app/controllers/otus_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

      create returns a model which is always truthy.
      Open

            if @result.create
      Severity: Minor
      Found in app/controllers/otus_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

      create returns a model which is always truthy.
      Open

            if @result.create
      Severity: Minor
      Found in app/controllers/otus_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

      create returns a model which is always truthy.
      Open

            if @result.create
      Severity: Minor
      Found in app/controllers/otus_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

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

          @otu.destroy
      Severity: Minor
      Found in app/controllers/otus_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

      TODO found
      Open

              flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} TODO RECORD TYPES were created."
      Severity: Minor
      Found in app/controllers/otus_controller.rb by fixme

      TODO found
      Open

        # TODO: Considerations
      Severity: Minor
      Found in app/controllers/otus_controller.rb by fixme

      TODO found
      Open

        # TODO: AUTOGENERATED STUB, check and update
      Severity: Minor
      Found in app/controllers/otus_controller.rb by fixme

      TODO found
      Open

        # TODO: AUTOGENERATED STUB, check and update
      Severity: Minor
      Found in app/controllers/otus_controller.rb by fixme

      TODO found
      Open

        # TODO: Redirect to json if too big?
      Severity: Minor
      Found in app/controllers/otus_controller.rb by fixme

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

        def api_index
    q = ::Queries::Otu::Filter.new(params.merge!(api: true)).all
      .where(project_id: sessions_current_project_id)
      .order('otus.id')
      Severity: Major
      Found in app/controllers/otus_controller.rb and 1 other location - About 1 hr to fix
      app/controllers/taxon_names_controller.rb on lines 241..257

      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 65.

      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 10 locations. Consider refactoring.
      Open

        def create_data_attributes_batch_load
    if params[:file] && digested_cookie_exists?(params[:file].tempfile, :data_attributes_batch_load_otus_md5)
      @result = BatchLoad::Import::Otus::DataAttributesInterpreter.new(**batch_params)
      if @result.create
        flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} TODO RECORD TYPES were created."
      Severity: Major
      Found in app/controllers/otus_controller.rb and 9 other locations - About 1 hr to fix
      app/controllers/collecting_events_controller.rb on lines 206..219
      app/controllers/collecting_events_controller.rb on lines 233..246
      app/controllers/collection_objects_controller.rb on lines 311..324
      app/controllers/collection_objects_controller.rb on lines 337..350
      app/controllers/descriptors_controller.rb on lines 162..177
      app/controllers/namespaces_controller.rb on lines 116..129
      app/controllers/sequences_controller.rb on lines 141..154
      app/controllers/sequences_controller.rb on lines 167..180
      app/controllers/taxon_names_controller.rb on lines 199..212

      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

      Similar blocks of code found in 16 locations. Consider refactoring.
      Open

        def destroy
    @otu.destroy
    respond_to do |format|
      if @otu.destroyed?
        format.html { destroy_redirect @otu, notice: 'OTU was successfully destroyed.' }
      Severity: Major
      Found in app/controllers/otus_controller.rb and 15 other locations - About 1 hr to fix
      app/controllers/citations_controller.rb on lines 86..94
      app/controllers/collecting_events_controller.rb on lines 82..90
      app/controllers/containers_controller.rb on lines 71..79
      app/controllers/contents_controller.rb on lines 67..75
      app/controllers/controlled_vocabulary_terms_controller.rb on lines 63..71
      app/controllers/descriptors_controller.rb on lines 84..92
      app/controllers/downloads_controller.rb on lines 36..44
      app/controllers/georeferences_controller.rb on lines 123..131
      app/controllers/observations_controller.rb on lines 92..100
      app/controllers/people_controller.rb on lines 71..79
      app/controllers/sequence_relationships_controller.rb on lines 66..74
      app/controllers/tags_controller.rb on lines 91..99
      app/controllers/taxon_name_classifications_controller.rb on lines 92..100
      app/controllers/taxon_name_relationships_controller.rb on lines 73..81
      app/controllers/taxon_names_controller.rb on lines 73..81

      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

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

        def preview_simple_batch_file_load
    if params[:files]
      @result = BatchFileLoad::Import::Otus::SimpleInterpreter.new(**batch_params)
      digest_cookie(params[:files][0].tempfile, :batch_file_load_simple_md5)
      render 'otus/batch_file_load/simple/preview'
      Severity: Minor
      Found in app/controllers/otus_controller.rb and 1 other location - About 35 mins to fix
      app/controllers/sequences_controller.rb on lines 104..112

      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 35.

      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 = Otu.batch_update(
        preview: params[:preview],
        otu: otu_params.merge(by: sessions_current_user_id),
        otu_query: params[:otu_query],
      Severity: Major
      Found in app/controllers/otus_controller.rb and 4 other locations - About 35 mins to fix
      app/controllers/asserted_distributions_controller.rb on lines 117..126
      app/controllers/biological_associations_controller.rb on lines 153..161
      app/controllers/collecting_events_controller.rb on lines 128..136
      app/controllers/collection_objects_controller.rb on lines 402..410

      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

        def preview_simple_batch_load
    if params[:file]
      @result = BatchLoad::Import::Otus.new(**batch_params.merge(user_map))
      digest_cookie(params[:file].tempfile, :batch_otus_md5)
      render('otus/batch_load/simple/preview')
      Severity: Minor
      Found in app/controllers/otus_controller.rb and 1 other location - About 35 mins to fix
      app/controllers/collection_objects_controller.rb on lines 268..276

      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 13 locations. Consider refactoring.
      Open

        def preview_identifiers_batch_load
    if params[:file]
      @result = BatchLoad::Import::Otus::IdentifiersInterpreter.new(**batch_params)
      digest_cookie(params[:file].tempfile, :batch_load_otus_identifiers_md5)
      render('otus/batch_load/identifiers/preview')
      Severity: Major
      Found in app/controllers/otus_controller.rb and 12 other locations - About 30 mins to fix
      app/controllers/collecting_events_controller.rb on lines 195..203
      app/controllers/collecting_events_controller.rb on lines 221..230
      app/controllers/collection_objects_controller.rb on lines 300..308
      app/controllers/collection_objects_controller.rb on lines 326..334
      app/controllers/descriptors_controller.rb on lines 121..129
      app/controllers/descriptors_controller.rb on lines 132..140
      app/controllers/namespaces_controller.rb on lines 105..113
      app/controllers/otus_controller.rb on lines 208..216
      app/controllers/sequence_relationships_controller.rb on lines 92..100
      app/controllers/sequences_controller.rb on lines 130..138
      app/controllers/sequences_controller.rb on lines 156..164
      app/controllers/taxon_names_controller.rb on lines 188..196

      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 13 locations. Consider refactoring.
      Open

        def preview_data_attributes_batch_load
    if params[:file]
      @result = BatchLoad::Import::Otus::DataAttributesInterpreter.new(**batch_params)
      digest_cookie(params[:file].tempfile, :data_attributes_batch_load_otus_md5)
      render 'otus/batch_load/data_attributes/preview'
      Severity: Major
      Found in app/controllers/otus_controller.rb and 12 other locations - About 30 mins to fix
      app/controllers/collecting_events_controller.rb on lines 195..203
      app/controllers/collecting_events_controller.rb on lines 221..230
      app/controllers/collection_objects_controller.rb on lines 300..308
      app/controllers/collection_objects_controller.rb on lines 326..334
      app/controllers/descriptors_controller.rb on lines 121..129
      app/controllers/descriptors_controller.rb on lines 132..140
      app/controllers/namespaces_controller.rb on lines 105..113
      app/controllers/otus_controller.rb on lines 156..164
      app/controllers/sequence_relationships_controller.rb on lines 92..100
      app/controllers/sequences_controller.rb on lines 130..138
      app/controllers/sequences_controller.rb on lines 156..164
      app/controllers/taxon_names_controller.rb on lines 188..196

      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

      Prefer symbols instead of strings as hash keys.
      Open

          {user_header_map: {'otu' => 'otu_name'}}
      Severity: Minor
      Found in app/controllers/otus_controller.rb by rubocop

      This cop checks for the use of strings as keys in hashes. The use of symbols is preferred instead.

      Example:

      # bad
{ 'one' => 1, 'two' => 2, 'three' => 3 }

# good
{ one: 1, two: 2, three: 3 }

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