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SysMO-DB/seek

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app/controllers/specimens_controller.rb

Summary

Maintainability
B
6 hrs
Test Coverage

Method create has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def create
    organism_id = params[:specimen].delete(:organism_id)
    @specimen = new_specimen
    sop_ids = (params[:specimen_sop_ids].nil? ? [] : params[:specimen_sop_ids].reject(&:blank?))||[]
    @specimen.build_sop_masters sop_ids
Severity: Minor
Found in app/controllers/specimens_controller.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 update has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def update
    sop_ids = (params[:specimen_sop_ids].nil?? [] : params[:specimen_sop_ids].reject(&:blank?))||[]
    @specimen.build_sop_masters sop_ids

    @specimen.attributes = params[:specimen]
Severity: Minor
Found in app/controllers/specimens_controller.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 new_specimen has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

  def new_specimen
        specimen = Specimen.new
        # to delete id hash which is saved in the hidden id field (automatically generated in form with fields_for)
          #delete id hashes of genotypes/phenotypes
          params[:specimen][:genotypes_attributes].try(:delete, "id")
Severity: Minor
Found in app/controllers/specimens_controller.rb - About 45 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 destroy has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def destroy
    respond_to do |format|
      if @specimen.destroy
        format.html { redirect_to(specimens_path) }
        format.xml { head :ok }
Severity: Minor
Found in app/controllers/specimens_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

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

    if @specimen.save
      if @specimen.from_biosamples=='true'
        #reload to get updated nested attributes,e.g. genotypes/phenotypes
        @specimen.reload
        render :partial => "biosamples/back_to_biosamples", :locals => {:action => 'update', :object => @specimen}
Severity: Major
Found in app/controllers/specimens_controller.rb and 1 other location - About 1 hr to fix
app/controllers/specimens_controller.rb on lines 65..80

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 53.

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

    if @specimen.save
      if @specimen.from_biosamples=='true'
        #reload to get updated nested attributes,e.g. genotypes/phenotypes
        @specimen.reload
        render :partial => "biosamples/back_to_biosamples", :locals => {:action => 'create', :object => @specimen}
Severity: Major
Found in app/controllers/specimens_controller.rb and 1 other location - About 1 hr to fix
app/controllers/specimens_controller.rb on lines 108..122

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 53.

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

        flash.now[:error]="Unable to delete the specimen" if !@specimen.institution.nil?
        format.html { render :action=>"show" }
        format.xml { render :xml => @specimen.errors, :status => :unprocessable_entity }
Severity: Minor
Found in app/controllers/specimens_controller.rb and 1 other location - About 20 mins to fix
app/controllers/assays_controller.rb on lines 236..238

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 28.

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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