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Method create has a Cognitive Complexity of 47 (exceeds 5 allowed). Consider refactoring.
Open

  def create
    @project = Project.find_by(id: query_dataset_params[:project_id])
    if @project.nil?
      redirect_to projects_path
    else
Severity: Minor
Found in app/controllers/query_datasets_controller.rb - About 7 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 projects_controller.rb has 468 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'miga'
require 'miga/daemon'

class ProjectsController < ApplicationController
  before_action :set_project,
Severity: Minor
Found in app/controllers/projects_controller.rb - About 7 hrs to fix

    Class ProjectsController has 35 methods (exceeds 20 allowed). Consider refactoring.
    Open

    class ProjectsController < ApplicationController
  before_action :set_project,
    only: [:destroy, :show, :search, :reference_datasets,
      :medoid_clade, :medoid_clade_as,
      :rdp_classify, :rdp_classify_as, :new_ncbi_download,
    Severity: Minor
    Found in app/controllers/projects_controller.rb - About 4 hrs to fix

      Method aai_intax has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
      Open

        def aai_intax(aai, project, ds_miga)
    opts = {}
    if project.miga && project.miga.metadata[:aai_p]
      opts[:engine] = project.miga.metadata[:aai_p]
    end
      Severity: Minor
      Found in app/helpers/query_datasets_helper.rb - About 3 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 21 (exceeds 5 allowed). Consider refactoring.
      Open

        def create
    @user = User.find_by(id: params[:user_id])
    par = project_params
    par[:official] = false unless @user.admin?
    @project = @user.projects.create(par)
      Severity: Minor
      Found in app/controllers/projects_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 list_query_datasets has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
      Open

        def list_query_datasets
    if params[:project_id]
      @project = Project.find(params[:project_id])
      qd = params[:all] ? @project.query_datasets.all :
            QueryDataset.by_user_and_project(current_user, @project)
      Severity: Minor
      Found in app/controllers/query_datasets_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_reference has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
      Open

        def create_reference
    cmd = params.require(:query_dataset).permit(
      :name, :input_type, :input_file, :input_file_2
    )
    cmd.merge! params.permit(:type, :comments, :description)
      Severity: Minor
      Found in app/controllers/projects_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 53 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        def create
    @project = Project.find_by(id: query_dataset_params[:project_id])
    if @project.nil?
      redirect_to projects_path
    else
      Severity: Major
      Found in app/controllers/query_datasets_controller.rb - About 2 hrs to fix

        Method plot_quality has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
        Open

          def plot_quality(comp, cont, qual)
    css_class = ["success","info","warning","danger"]
    comp_l = comp > 80.0 ? 0 : comp > 50.0 ? 1 : comp > 20.0 ? 2 : 3
    cont_l = cont <  4.0 ? 0 : cont < 10.0 ? 1 : cont < 16.0 ? 2 : 3
    qual_l = qual > 80.0 ? 0 : qual > 50.0 ? 1 : qual > 20.0 ? 2 : 3
        Severity: Minor
        Found in app/helpers/application_helper.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 result has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
        Open

          def result
    qd  = @query_dataset
    m   = qd.miga
    res = m.result(params[:result])
    if res.nil?
        Severity: Minor
        Found in app/controllers/query_datasets_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 aai_intax has 47 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          def aai_intax(aai, project, ds_miga)
    opts = {}
    if project.miga && project.miga.metadata[:aai_p]
      opts[:engine] = project.miga.metadata[:aai_p]
    end
        Severity: Minor
        Found in app/helpers/query_datasets_helper.rb - About 1 hr to fix

          Method create_reference has 44 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

            def create_reference
    cmd = params.require(:query_dataset).permit(
      :name, :input_type, :input_file, :input_file_2
    )
    cmd.merge! params.permit(:type, :comments, :description)
          Severity: Minor
          Found in app/controllers/projects_controller.rb - About 1 hr to fix

            Method discovery has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
            Open

              def discovery
    require 'miga/lair'
    require 'pathname'

    lair = MiGA::Lair.new(Settings.miga_projects)
            Severity: Minor
            Found in app/controllers/projects_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 search has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
            Open

              def search
    # Query
    @q       = params[:q]
    @query   = @q.split(/\s(?=(?:[^"]|"[^"]*")*$)/).map do |i|
      (i =~ /^(?:([A-Za-z_]+):)?"?(.*?)"?$/) ? [$2, $1] : [i, nil]
            Severity: Minor
            Found in app/controllers/projects_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 list_query_datasets has 40 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

              def list_query_datasets
    if params[:project_id]
      @project = Project.find(params[:project_id])
      qd = params[:all] ? @project.query_datasets.all :
            QueryDataset.by_user_and_project(current_user, @project)
            Severity: Minor
            Found in app/controllers/query_datasets_controller.rb - About 1 hr to fix

              Method progress has 40 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                def progress
    ref_ds = @project.miga.dataset_names.select { |i| i !~ /^qG_/ }
    status = ref_ds.sample(100).map do |i|
      @project.miga.dataset(i).status
    end
              Severity: Minor
              Found in app/controllers/projects_controller.rb - About 1 hr to fix

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

                  def plot_quality_deprecated(comp, cont, qual)
    cols = ["rgba(92,184,92,1)", "rgba(91,192,222,1)",
      "rgba(240,173,78,1)", "rgba(217,83,79,1)"]
    comp_l = comp > 80.0 ? 0 : comp > 50.0 ? 1 : comp > 20.0 ? 2 : 3
    cont_l = cont <  4.0 ? 0 : cont < 10.0 ? 1 : cont < 16.0 ? 2 : 3
                Severity: Minor
                Found in app/helpers/application_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 create_miga_dataset has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
                Open

                  def create_miga_dataset(par, file1, file2 = nil)
    require 'miga/cli'
    input_type = par[:input_type]
    input_type = 'trimmed_reads' if par[:input_type] == 'trimmed_fasta'
    input_type += file2 ? '_paired' : '_single' unless input_type == 'assembly'
                Severity: Minor
                Found in app/models/project.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 plot_quality has 31 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                  def plot_quality(comp, cont, qual)
    css_class = ["success","info","warning","danger"]
    comp_l = comp > 80.0 ? 0 : comp > 50.0 ? 1 : comp > 20.0 ? 2 : 3
    cont_l = cont <  4.0 ? 0 : cont < 10.0 ? 1 : cont < 16.0 ? 2 : 3
    qual_l = qual > 80.0 ? 0 : qual > 50.0 ? 1 : qual > 20.0 ? 2 : 3
                Severity: Minor
                Found in app/helpers/application_helper.rb - About 1 hr to fix

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

                    def estimated_wait_time(project_id)
    @estimated_wait_time_last_check ||= []
    @estimated_wait_time ||= []
    if @estimated_wait_time_last_check[project_id].nil? or
          @estimated_wait_time_last_check[project_id] < 48.hours.ago
                  Severity: Minor
                  Found in app/helpers/projects_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

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