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app/controllers/sequence_relationships_controller.rb

Summary

Maintainability
B
5 hrs
Test Coverage

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

  def create_primers_batch_load
    if params[:file] && digested_cookie_exists?(params[:file].tempfile, :Primers_sequences_md5)
      @result = BatchLoad::Import::SequenceRelationships::PrimersInterpreter.new(**batch_params)
      if @result.create!
        flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} " \
Severity: Minor
Found in app/controllers/sequence_relationships_controller.rb - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    @sequence_relationship.destroy
Severity: Minor
Found in app/controllers/sequence_relationships_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 2 locations. Consider refactoring.
Open

  def create_primers_batch_load
    if params[:file] && digested_cookie_exists?(params[:file].tempfile, :Primers_sequences_md5)
      @result = BatchLoad::Import::SequenceRelationships::PrimersInterpreter.new(**batch_params)
      if @result.create!
        flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} " \
Severity: Major
Found in app/controllers/sequence_relationships_controller.rb and 1 other location - About 1 hr to fix
app/controllers/descriptors_controller.rb on lines 143..160

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 50.

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
    @sequence_relationship.destroy
    respond_to do |format|
      if @sequence_relationship.destroyed?
        format.html { destroy_redirect @sequence_relationship, notice: 'Sequence relationship was successfully destroyed.' }
Severity: Major
Found in app/controllers/sequence_relationships_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/otus_controller.rb on lines 101..109
app/controllers/people_controller.rb on lines 71..79
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 update
    respond_to do |format|
      if @sequence_relationship.update(sequence_relationship_params)
        format.html { redirect_to url_for(@sequence_relationship.metamorphosize),
                                  notice: 'Sequence relationship was successfully updated.' }
Severity: Minor
Found in app/controllers/sequence_relationships_controller.rb and 1 other location - About 55 mins to fix
app/controllers/documentation_controller.rb on lines 54..62

Duplicated Code

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

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

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

Tuning

This issue has a mass of 46.

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

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

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

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

Refactorings

Further Reading

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

    respond_to do |format|
      if @sequence_relationship.save
        format.html { redirect_to sequence_relationship_path(@sequence_relationship),
                                  notice: 'Sequence relationship was successfully created.' }
        format.json { render :show, status: :created, location: @sequence_relationship }
Severity: Minor
Found in app/controllers/sequence_relationships_controller.rb and 1 other location - About 50 mins to fix
app/controllers/contents_controller.rb on lines 40..46

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 42.

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_primers_batch_load
    if params[:file]
      @result = BatchLoad::Import::SequenceRelationships::PrimersInterpreter.new(**batch_params)
      digest_cookie(params[:file].tempfile, :Primers_sequences_md5)
      render 'sequence_relationships/batch_load/primers/preview'
Severity: Major
Found in app/controllers/sequence_relationships_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/otus_controller.rb on lines 208..216
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

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