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Method fix_run_output_ports_mime_types has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

def fix_run_output_ports_mime_types(run)
  run.outputs.each do |output|
    output.metadata = {:size => nil, :type => ''} if output.metadata.nil?
    port = run.executed_workflow.output_ports.detect { |o| o.name == output.name }
    if port && !port.mime_type.blank?
Severity: Minor
Found in lib/taverna_player_callbacks.rb - About 55 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 update_subscription_job_if_study_or_assay has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def update_subscription_job_if_study_or_assay
    if self.kind_of?(Study) && self.investigation_id_changed?
      #update subscriptions for study
      old_investigation_id = self.investigation_id_was
      old_investigation = Investigation.find_by_id old_investigation_id
Severity: Minor
Found in lib/subscribable.rb - About 55 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

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

         if chebi_ids.blank?
           kegg_ids.each do |kegg_id|
             mapping = new_or_update_mapping sabiork_id, nil, kegg_id
             mapping_links.push MappingLink.new(:substance => compound, :mapping => mapping)
           end
Severity: Minor
Found in lib/seek/factor_studied.rb and 1 other location - About 55 mins to fix
lib/seek/factor_studied.rb on lines 161..171

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 45.

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

         if chebi_ids.blank?
           kegg_ids.each do |kegg_id|
             mapping = new_or_update_mapping sabiork_id, nil, kegg_id
             mapping_links.push MappingLink.new(:substance => compound, :mapping => mapping)
           end
Severity: Minor
Found in lib/seek/factor_studied.rb and 1 other location - About 55 mins to fix
lib/seek/factor_studied.rb on lines 134..144

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 45.

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

    @t2flow.sources.each do |source|
      unless @workflow.input_ports.detect { |i| i.name == source.name && i.workflow_version == @workflow.version }
        @workflow.input_ports.build(:name => source.name,
                                    :description => (source.descriptions || []).last,
                                    :example_value => (source.example_values || []).last,
Severity: Minor
Found in app/controllers/workflows_controller.rb and 1 other location - About 55 mins to fix
app/controllers/workflows_controller.rb on lines 271..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 45.

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

    @t2flow.sinks.each do |sink|
      unless @workflow.output_ports.detect { |o| o.name == sink.name && o.workflow_version == @workflow.version }
        @workflow.output_ports.build(:name => sink.name,
                                     :description => (sink.descriptions || []).last,
                                     :example_value => (sink.example_values || []).last,
Severity: Minor
Found in app/controllers/workflows_controller.rb and 1 other location - About 55 mins to fix
app/controllers/workflows_controller.rb on lines 262..267

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 45.

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 destroy
    @help_image = HelpImage.find(params[:id])
    @help_document = HelpDocument.find_by_identifier(params[:help_document_id])
    @help_image.destroy
    render :update do |page|
Severity: Minor
Found in app/controllers/help_images_controller.rb and 1 other location - About 55 mins to fix
app/controllers/help_attachments_controller.rb on lines 29..36

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 45.

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 destroy
    @help_attachment = HelpAttachment.find(params[:id])
    @help_document = HelpDocument.find_by_identifier(params[:help_document_id])
    @help_attachment.destroy
    render :update do |page|
Severity: Minor
Found in app/controllers/help_attachments_controller.rb and 1 other location - About 55 mins to fix
app/controllers/help_images_controller.rb on lines 24..31

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 45.

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(direction == 'next'){
                slider.settings.onSlideNext(slider.children.eq(slider.active.index), slider.oldIndex, slider.active.index);
            }else if(direction == 'prev'){
                slider.settings.onSlidePrev(slider.children.eq(slider.active.index), slider.oldIndex, slider.active.index);
            }
Severity: Minor
Found in app/assets/javascripts/jquery.bxslider.js and 1 other location - About 55 mins to fix
app/assets/javascripts/jquery.bxslider.js on lines 1116..1118

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

            }else if(direction == 'prev'){
                slider.settings.onSlidePrev(slider.children.eq(slider.active.index), slider.oldIndex, slider.active.index);
            }
Severity: Minor
Found in app/assets/javascripts/jquery.bxslider.js and 1 other location - About 55 mins to fix
app/assets/javascripts/jquery.bxslider.js on lines 1114..1118

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

      respond_to do |format|
        if saved
          flash[:notice] = "#{t('assays.assay')} type was successfully created."
          format.html { redirect_to(:action => "manage") }
          format.xml { head :ok }
Severity: Minor
Found in app/controllers/suggested_assay_types_controller.rb and 1 other location - About 55 mins to fix
app/controllers/suggested_assay_types_controller.rb on lines 93..100

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 3 locations. Consider refactoring.
Open

  def request_resource
    resource = Model.find(params[:id])
    details = params[:details]

    Mailer.request_resource(current_user,resource,details,base_host).deliver
Severity: Major
Found in app/controllers/models_controller.rb and 2 other locations - About 55 mins to fix
app/controllers/data_files_controller.rb on lines 355..362
app/controllers/sops_controller.rb on lines 203..210

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 2 locations. Consider refactoring.
Open

        sample.tissue_and_cell_types.each do |tt|
          result += "[" if tt== sample.tissue_and_cell_types.first
          result += link_to h(tt.title), tt
          result += "|" unless tt == sample.tissue_and_cell_types.last
          result += "]" if tt == sample.tissue_and_cell_types.last
Severity: Minor
Found in app/helpers/assays_helper.rb and 1 other location - About 55 mins to fix
app/helpers/samples_helper.rb on lines 34..38

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 2 locations. Consider refactoring.
Open

      respond_to do |format|
        if saved
          flash[:notice] = "#{t('assays.assay')} type was successfully updated."
          format.html { redirect_to(:action => "manage") }
          format.xml { head :ok }
Severity: Minor
Found in app/controllers/suggested_assay_types_controller.rb and 1 other location - About 55 mins to fix
app/controllers/suggested_assay_types_controller.rb on lines 63..70

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 2 locations. Consider refactoring.
Open

        sample.tissue_and_cell_types.each do |tt|
          result += " [" if tt== sample.tissue_and_cell_types.first
          result += link_to h(tt.title), tt
          result += " | " unless tt == sample.tissue_and_cell_types.last
          result += "]" if tt == sample.tissue_and_cell_types.last
Severity: Minor
Found in app/helpers/samples_helper.rb and 1 other location - About 55 mins to fix
app/helpers/assays_helper.rb on lines 70..74

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 3 locations. Consider refactoring.
Open

  def request_resource
    resource = Sop.find(params[:id])
    details = params[:details]
    
    Mailer.request_resource(current_user,resource,details,base_host).deliver
Severity: Major
Found in app/controllers/sops_controller.rb and 2 other locations - About 55 mins to fix
app/controllers/data_files_controller.rb on lines 355..362
app/controllers/models_controller.rb on lines 488..495

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 3 locations. Consider refactoring.
Open

  def request_resource
    resource = DataFile.find(params[:id])
    details = params[:details]
    
    Mailer.request_resource(current_user,resource,details,base_host).deliver
Severity: Major
Found in app/controllers/data_files_controller.rb and 2 other locations - About 55 mins to fix
app/controllers/models_controller.rb on lines 488..495
app/controllers/sops_controller.rb on lines 203..210

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

Function addOrganism has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

function addOrganism(title,id,strain_info,strain_id,culture_growth,t_id,t_title) {
Severity: Major
Found in app/assets/javascripts/assays.js - About 50 mins to fix

    Function roundRectangleIntersectLine has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

            x, y, nodeX, nodeY, width, height, padding) {
    Severity: Major
    Found in app/assets/javascripts/modified_cytoscape.js - About 50 mins to fix

      Method tree_editor_display has 7 arguments (exceeds 4 allowed). Consider refactoring.
      Open

        def tree_editor_display type, show_edit=true, show_delete=true, selected_id=nil, related_resource_type="Person",selective_display=false, foldable=false
      Severity: Major
      Found in app/helpers/projects_helper.rb - About 50 mins to fix
        Severity
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