Sign upLogin

SysMO-DB/seek

View on GitHub
Star
app/controllers/data_files_controller.rb

Summary

Maintainability
D
3 days
Test Coverage

Method create has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.
Open

  def create
    if handle_upload_data

      @data_file = DataFile.new params[:data_file]
Severity: Minor
Found in app/controllers/data_files_controller.rb - About 5 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

File data_files_controller.rb has 313 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'simple-spreadsheet-extractor'

class DataFilesController < ApplicationController

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

    Method new_version has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
    Open

      def new_version
    if handle_upload_data
      comments=params[:revision_comment]

      respond_to do |format|
    Severity: Minor
    Found in app/controllers/data_files_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 update has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

      def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:data_file]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:data_file].delete(column_name)
    Severity: Minor
    Found in app/controllers/data_files_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 upload_from_email has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
    Open

      def upload_from_email
    if current_user.is_admin? && Seek::Config.admin_impersonation_enabled
      User.with_current_user Person.find(params[:sender_id]).user do
        if handle_upload_data
          @data_file = DataFile.new params[:data_file]
    Severity: Minor
    Found in app/controllers/data_files_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 43 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

      def create
    if handle_upload_data

      @data_file = DataFile.new params[:data_file]
    Severity: Minor
    Found in app/controllers/data_files_controller.rb - About 1 hr to fix

      Method update has 43 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[:data_file]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:data_file].delete(column_name)
      Severity: Minor
      Found in app/controllers/data_files_controller.rb - About 1 hr to fix

        Method new_version has 28 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          def new_version
    if handle_upload_data
      comments=params[:revision_comment]

      respond_to do |format|
        Severity: Minor
        Found in app/controllers/data_files_controller.rb - About 1 hr to fix

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

            def upload_for_tool

    if handle_upload_data
      params[:data_file][:project_ids] = [params[:data_file].delete(:project_id)] if params[:data_file][:project_id]
      @data_file = DataFile.new params[:data_file]
          Severity: Minor
          Found in app/controllers/data_files_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

          Avoid deeply nested control flow statements.
          Open

                        unless  bio_samples.errors.blank?
                flash[:notice] << "<br/> However, Sample database population failed."
                flash[:error] = bio_samples.errors.html_safe
                #respond_to do |format|
                #  format.html{
          Severity: Major
          Found in app/controllers/data_files_controller.rb - About 45 mins to fix

            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

            Similar blocks of code found in 8 locations. Consider refactoring.
            Open

              def preview
    element=params[:element]
    data_file=DataFile.find_by_id(params[:id])
    
    render :update do |page|
            Severity: Major
            Found in app/controllers/data_files_controller.rb and 7 other locations - About 35 mins to fix
            app/controllers/assays_controller.rb on lines 249..258
            app/controllers/events_controller.rb on lines 96..105
            app/controllers/models_controller.rb on lines 474..484
            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[:data_file]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:data_file].delete(column_name)
      end
            Severity: Minor
            Found in app/controllers/data_files_controller.rb and 4 other locations - About 25 mins to fix
            app/controllers/models_controller.rb on lines 407..413
            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

            There are no issues that match your filters.

            Category
            Status