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

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

Open

  def create
     user = User.find_by(email: params[:session][:email].downcase)
     if user && user.authenticate(params[:session][:password])
    if user.activated?
       # Log the user in and redirect to the user's show page.

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

Open

  def link_to_reference_dataset(project, dataset_name)
    pm = project.miga if project
    ds_miga = pm.dataset(dataset_name) if pm
    if ds_miga.nil?
      content_tag(:del, dataset_name, title: 'Reference dataset removed')

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Method result has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def result
    qd  = @query_dataset
    m   = qd.miga
    res = m.result(params[:result])
    if res.nil?

Method aai_novel has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def aai_novel(aai, project)
    opts = {}
    if project.miga && project.miga.metadata[:aai_p]
      opts[:engine] = project.miga.metadata[:aai_p]
    end

Method plot_assembly has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def plot_assembly(n50, len)
    # Trace1: RefSeq genomes
    trace1 = {
      x: [298471,2240716,3402093,4653910,13033779],
      type: "box",

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 display_data has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def display_data(obj, html_safe = false)
    case obj
    when Float
      obj.round(2).to_s
    when Array

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Avoid deeply nested control flow statements.

Open

            if saved_cnt == 1
              redirect_to @query_dataset
            else
              redirect_to project_query_datasets_url(@project)
            end

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

Open

  def create_miga_dataset
    # Don't do anything if it already exists
    return true if project.miga.dataset(miga_name)

    err = project.create_miga_dataset(

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

Open

   def current_user
      if (user_id = session[:user_id])
     @current_user ||= User.find_by(id: user_id)
      elsif (user_id = cookies.signed[:user_id])
     user = User.find_by(id: user_id)

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

Open

  def create
    par = user_params
    if User.all.empty?
      par[:activated] = true
      par[:activated_at] = Time.zone.now

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

Open

  def rdp_classify(ds_name)
    ds_miga = miga.dataset(ds_name)
    return if ds_miga.nil?
    res = ds_miga.result(:ssu)
    return if res.nil?

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