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,

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,

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)

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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)

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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)

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)

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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]

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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

Method create has 26 lines of code (exceeds 25 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)

Method launch_get_db has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def launch_get_db
    name = params[:name]
    version = params[:version]
    Thread.new do
      require 'miga/cli'

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Method reference_dataset_result has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

  def reference_dataset_result
    if p = @project and m = p.miga
      if ds = m.dataset(params[:dataset]) and res = ds.result(params[:result])
        if file = res.data[:files][params[:file].to_sym]
          send_result(file, res)

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Method result_partial has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

  def result_partial
    if params[:q_ds].nil?
      obj = @project
      proj = obj
      unless params[:r_ds].nil?

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Method get_db has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

  def get_db
    manif = Project.miga_online_manif
    @downloadable = manif[:databases].map do |name, i|
      local = Project.find_by(path: name)
      local_v = (local.miga.metadata[:release] || 'unknown') if local && local.miga

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Method send_result has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

  def send_result(file, res)
    f = File.expand_path(file, res.dir)
    if Dir.exist? f and params[:f] and not params[:f]=~/\//
      f = File.expand_path(params[:f], f)
      file = params[:f]

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