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app/controllers/models_controller.rb

Summary

Maintainability
F
4 days
Test Coverage

File models_controller.rb has 452 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'libxml'
require 'bives'

class ModelsController < ApplicationController
Severity: Minor
Found in app/controllers/models_controller.rb - About 6 hrs to fix

    Method submit_to_jws has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.
    Open

      def submit_to_jws
    following_action=params.delete("following_action")
    error=nil

    #FIXME: currently we have to assume that a model with multiple files only contains 1 model file that would be executed on jws online, and only the first one is chosen
    Severity: Minor
    Found in app/controllers/models_controller.rb - About 4 hrs 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

    Class ModelsController has 28 methods (exceeds 20 allowed). Consider refactoring.
    Open

    class ModelsController < ApplicationController

  include WhiteListHelper
  include IndexPager
  include DotGenerator
    Severity: Minor
    Found in app/controllers/models_controller.rb - About 3 hrs to fix

      Method update has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
      Open

        def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:model]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:model].delete(column_name)
      Severity: Minor
      Found in app/controllers/models_controller.rb - About 2 hrs 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 create has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
      Open

        def create
    if handle_upload_data
      @model = Model.new(params[:model])

      @model.policy.set_attributes_with_sharing params[:sharing], @model.projects
      Severity: Minor
      Found in app/controllers/models_controller.rb - About 2 hrs 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 submit_to_jws has 54 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        def submit_to_jws
    following_action=params.delete("following_action")
    error=nil

    #FIXME: currently we have to assume that a model with multiple files only contains 1 model file that would be executed on jws online, and only the first one is chosen
      Severity: Major
      Found in app/controllers/models_controller.rb - About 2 hrs to fix

        Method update has 39 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:model]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:model].delete(column_name)
        Severity: Minor
        Found in app/controllers/models_controller.rb - About 1 hr to fix

          Method builder has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
          Open

            def builder
    saved_file=params[:saved_file]
    error=nil
    supported=false
    begin
          Severity: Minor
          Found in app/controllers/models_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 builder has 30 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

            def builder
    saved_file=params[:saved_file]
    error=nil
    supported=false
    begin
          Severity: Minor
          Found in app/controllers/models_controller.rb - About 1 hr to fix

            Method create has 29 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

              def create
    if handle_upload_data
      @model = Model.new(params[:model])

      @model.policy.set_attributes_with_sharing params[:sharing], @model.projects
            Severity: Minor
            Found in app/controllers/models_controller.rb - About 1 hr to fix

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

                def compare_versions
    if params[:file_id]
      @blob1 = @display_model.sbml_content_blobs.find{|b| b.id.to_s == params[:file_id]}
    else
      @blob1 = @display_model.sbml_content_blobs.first
              Severity: Minor
              Found in app/controllers/models_controller.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 simulate has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
              Open

               def simulate
    error=nil
    begin
      if @display_model.is_jws_supported?
        @modelname = Seek::JWS::Simulator.new.simulate(@display_model.jws_supported_content_blobs.first)
              Severity: Minor
              Found in app/controllers/models_controller.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 delete_model_type has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

                def delete_model_type params
    id=params[:selected_model_type_id]
    model_type=ModelType.find(id)
    success=false
    if (model_type.models.empty?)
              Severity: Minor
              Found in app/controllers/models_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 submit_to_sycamore has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

                def submit_to_sycamore
    @model = Model.find_by_id(params[:id])
    @display_model = @model.find_version(params[:version])
    error_message = nil
    if !Seek::Config.sycamore_enabled
              Severity: Minor
              Found in app/controllers/models_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 delete_model_format has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

                def delete_model_format params
    id=params[:selected_model_format_id]
    model_format=ModelFormat.find(id)
    success=false
    if (model_format.models.empty?)
              Severity: Minor
              Found in app/controllers/models_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

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

                def delete_model_type params
    id=params[:selected_model_type_id]
    model_type=ModelType.find(id)
    success=false
    if (model_type.models.empty?)
              Severity: Major
              Found in app/controllers/models_controller.rb and 1 other location - About 2 hrs to fix
              app/controllers/models_controller.rb on lines 298..318

              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 82.

              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 delete_model_format params
    id=params[:selected_model_format_id]
    model_format=ModelFormat.find(id)
    success=false
    if (model_format.models.empty?)
              Severity: Major
              Found in app/controllers/models_controller.rb and 1 other location - About 2 hrs to fix
              app/controllers/models_controller.rb on lines 273..293

              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 82.

              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 @model.save

        # update attributions
        Relationship.create_or_update_attributions(@model, params[:attributions])
              Severity: Major
              Found in app/controllers/models_controller.rb and 1 other location - About 2 hrs to fix
              app/controllers/presentations_controller.rb on lines 156..186

              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 80.

              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 8 locations. Consider refactoring.
              Open

                def preview

    element = params[:element]
    model = Model.find_by_id(params[:id])
              Severity: Major
              Found in app/controllers/models_controller.rb and 7 other locations - About 35 mins to fix
              app/controllers/assays_controller.rb on lines 249..258
              app/controllers/data_files_controller.rb on lines 342..351
              app/controllers/events_controller.rb on lines 96..105
              app/controllers/presentations_controller.rb on lines 202..212
              app/controllers/samples_controller.rb on lines 214..224
              app/controllers/sops_controller.rb on lines 189..199
              app/controllers/workflows_controller.rb on lines 171..180

              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 36.

              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

                  if params[:model]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:model].delete(column_name)
      end
              Severity: Minor
              Found in app/controllers/models_controller.rb and 4 other locations - About 25 mins to fix
              app/controllers/data_files_controller.rb on lines 257..263
              app/controllers/presentations_controller.rb on lines 134..140
              app/controllers/sops_controller.rb on lines 126..132
              app/controllers/workflows_controller.rb on lines 108..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 29.

              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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