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SysMO-DB/seek

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app/helpers/biosamples_helper.rb

Summary

Maintainability
B
4 hrs
Test Coverage

Method specimen_row_data has 41 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def specimen_row_data specimen
    id_column = Seek::Config.is_virtualliver ? 8 : 6
    creators = []
    specimen.creators.each do |creator|
      creators << link_to(h(creator.name), person_path(creator.id))
Severity: Minor
Found in app/helpers/biosamples_helper.rb - About 1 hr to fix

    Method specimen_row_data has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
    Open

      def specimen_row_data specimen
    id_column = Seek::Config.is_virtualliver ? 8 : 6
    creators = []
    specimen.creators.each do |creator|
      creators << link_to(h(creator.name), person_path(creator.id))
    Severity: Minor
    Found in app/helpers/biosamples_helper.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 strain_row_data has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

      def strain_row_data strain
    creator = strain.contributor.try(:person)
    creator_link = creator ? link_to(creator.name, person_path(creator.id)) : ""
    parent_strain_link = strain.parent.nil? ? nil : link_to(h(strain.parent.title),strain.parent)
    [(link_to h(strain.organism.title), organism_path(strain.organism.id)),
    Severity: Minor
    Found in app/helpers/biosamples_helper.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 strain.can_delete?
        link_to image("destroy", :alt => "Delete", :title => "Delete this strain"), {:action => "destroy", :controller => 'biosamples', :id => strain.id, :class => 'strain', :id_column_position => 5},
                             :confirm => "Are you sure you want to delete this strain?", :method => :delete, :remote => true
      else
    Severity: Minor
    Found in app/helpers/biosamples_helper.rb and 1 other location - About 20 mins to fix
    app/helpers/biosamples_helper.rb on lines 122..124

    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 27.

    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

        delete_icon = sample.can_delete? ? (link_to image("destroy", :alt => "Delete", :title => "Delete this sample"),
                             {:action => "destroy", :controller => 'biosamples', :id => sample.id, :class => 'sample', :id_column_position => 6},
                             :confirm => "Are you sure you want to delete this sample?", :method => :delete, :remote => true) : disabled_delete_icon
    Severity: Minor
    Found in app/helpers/biosamples_helper.rb and 1 other location - About 20 mins to fix
    app/helpers/biosamples_helper.rb on lines 29..32

    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 27.

    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

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

               (check_box_tag "selected_specimen_#{specimen.id}", specimen.id, false, {:onchange => remote_function(:url => {:controller => 'biosamples',
                                                                                                                         :action => 'existing_samples'},
                                                                                                                        :method => :get,
                                                                                                                        :with => "'specimen_ids=' + getSelectedSpecimens()",
                                                                                                                        :before=>"show_large_ajax_loader('existing_samples')") + ";show_existing_samples();"}),
    Severity: Minor
    Found in app/helpers/biosamples_helper.rb and 1 other location - About 15 mins to fix
    app/helpers/biosamples_helper.rb on lines 100..104

    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 26.

    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

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

           (check_box_tag "selected_specimen_#{specimen.id}", specimen.id, false, {:onchange => remote_function(:url => {:controller => 'biosamples',
                                                                                                                     :action => 'existing_samples'},
                                                                                                                    :method => :get,
                                                                                                                    :with => "'specimen_ids=' + getSelectedSpecimens()",
                                                                                                                    :before=>"show_large_ajax_loader('existing_samples')") + ";show_existing_samples();"}),
    Severity: Minor
    Found in app/helpers/biosamples_helper.rb and 1 other location - About 15 mins to fix
    app/helpers/biosamples_helper.rb on lines 109..113

    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 26.

    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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