Method create has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @user_phenotype = current_user.user_picture_phenotypes.new(
      phenotype_picture: params[:user_picture_phenotype][:phenotype_picture])
    @user_phenotype.phenotype_picture = params[:user_picture_phenotype][:phenotype_picture]
    @user_phenotype.user_id = current_user.id

Method process_row has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def process_row(row)
    snp_name = row[21]
    pvalue   = row[27].to_f
    snp      = Snp.find_by_name(snp_name)
    return unless snp && pvalue < 1e-8 && known_snps.include?(snp_name.downcase)

Method index has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def index
    # showing all users
    # TODO: Refactor this. - Helge
    @users = User.order(sort_column + ' ' + sort_direction)
    @users_paginate = @users.paginate(page: params[:page], per_page: 10)

Method process_documents has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def process_documents(documents)
    if documents.blank?
      logger.info("mendeley: No papers found")
      return
    end

Method create has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @user_phenotype = UserPhenotype.new(user_phenotype_params)
    @user_phenotype.user_id = current_user.id

    if params[:js_modal]

Method json_element has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def json_element(params)
    # TODO: Refactor this. - Helge
    @result = {}
    begin
      @snp = params[:snp] || Snp.find_by_name(params[:snp_name].downcase)

Method perform has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def perform(snp_id)
    Snp.reset_counters(snp_id, :user_snps)
    s = Snp.find(snp_id)
    s.allele_frequency ||= { "A" => 0, "T" => 0, "G" => 0, "C" => 0}
    s.genotype_frequency ||= {}

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

Open

  def perform(mendeley_paper_id)
     mendeley_paper = MendeleyPaper.find_by_id(mendeley_paper_id.to_i)
     return if mendeley_paper.nil?

     key_handle = File.open(::Rails.root.to_s+"/key_mendeley.txt")

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

Open

  def update
    @user = User.find(params[:id])

    if params[:user][:user_phenotypes_attributes].present?
      params[:user][:user_phenotypes_attributes].each do |p|

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

Open

    def call
      Genotype.includes(:user).find_each do |genotype|
        next unless File.exist?(genotype.genotype.path)

        user = genotype.user

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

Open

  def json_annotation
    result = {}
    if params[:snp_name].index(',')
      snps = params[:snp_name].split(',')
      snps.each do |s|

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Method create has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @phenotype_comment = PhenotypeComment.new(phenotype_comment_params)
    if @phenotype_comment.comment_text.index(/\A(\@\#\d*\:)/) == nil
      @phenotype_comment.reply_to_id = -1
    else

Method create has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @phenotype_comment = PicturePhenotypeComment.new(picture_phenotype_comment_params)
    if @phenotype_comment.comment_text.index(/\A(\@\#\d*\:)/) == nil
      @phenotype_comment.reply_to_id = -1
    else

Method parse_iyg has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def parse_iyg(rows)
    db_snp_names = {
      "MT-T3027C" => "rs199838004", "MT-T4336C" => "rs41456348",
      "MT-G4580A" => "rs28357975", "MT-T5004C" => "rs41419549",
      "MT-C5178a" => "rs28357984", "MT-A5390G" => "rs41333444",

Method create has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @snp_comment = SnpComment.new(comment_params)
    if @snp_comment.comment_text.index(/\A(\@\#\d*\:)/) == nil
      @snp_comment.reply_to_id = -1
    else

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

Open

  def perform(mendeley_paper_id)
     mendeley_paper = MendeleyPaper.find_by_id(mendeley_paper_id.to_i)
     return if mendeley_paper.nil?

     key_handle = File.open(::Rails.root.to_s+"/key_mendeley.txt")

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Avoid deeply nested control flow statements.

Open

      if l.strip.split(",").length == 6
        file_is_ok = true
        logger.info "file is decodeme and is ok!"
      end

Avoid deeply nested control flow statements.

Open

    elsif genotype.filetype == "ftdna-illumina"
      # first line is of length 4
      if l.strip.split(",").length == 4
        file_is_ok = true
        logger.info "file is ftdna and is ok!"

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

Open

  def create
    @genotype = Genotype.create(genotype_params)
    @genotype.user = current_user
    if @genotype.valid? && @genotype.save
      Preparsing.perform_async(@genotype.id)

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

Open

  def show
    @snp = Snp.includes(:snp_comments).
      where(name: params[:id].downcase).first || not_found

    if params[:format] == 'json'

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