SysMO-DB/seek

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

Open

  def index
    if (params[:discipline_id])
      @discipline=Discipline.find(params[:discipline_id])
      #FIXME: strips out the disciplines that don't match
      @people=Person.where(["disciplines.id=?",@discipline.id]).includes(:disciplines)

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

Open

  def builder
    saved_file=params[:saved_file]
    error=nil
    supported=false
    begin

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

Open

      def handle_download_zip asset
        #get the list of filename and filepath, {:filename => filepath}
        files_to_download = {}
        #store content_type for the case of 1 file
        content_type = nil

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

Open

  def create_from_existing
    experimental_condition_ids = []
    new_experimental_conditions = []
    #retrieve the selected FSes
    params.each do |key, value|

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

Open

    def add_breadcrumbs
      #Home
      add_breadcrumb "Home", :root_path
      #process for nested attributes
      if controller_name == 'studied_factors'

Similar blocks of code found in 2 locations. Consider refactoring.

Open

  def create
    @group = WorkGroup.new(params[:group])

    respond_to do |format|
      if @group.save

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    if @specimen.save
      if @specimen.from_biosamples=='true'
        #reload to get updated nested attributes,e.g. genotypes/phenotypes
        @specimen.reload
        render :partial => "biosamples/back_to_biosamples", :locals => {:action => 'create', :object => @specimen}

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

  def create
    @institution = Institution.new(params[:institution])

    respond_to do |format|
      if @institution.save

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    if @specimen.save
      if @specimen.from_biosamples=='true'
        #reload to get updated nested attributes,e.g. genotypes/phenotypes
        @specimen.reload
        render :partial => "biosamples/back_to_biosamples", :locals => {:action => 'update', :object => @specimen}

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Function select_cells has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function select_cells(startCol, startRow, endCol, endRow, sheetNumber) {
    var minRow = startRow;
    var minCol = startCol;
    var maxRow = endRow;
    var maxCol = endCol;

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

Open

  def authorized_list all_items, attribute, sort=true, max_length=75, count_hidden_items=false
    items = all_items.select &:can_view?
    if Seek::Config.is_virtualliver
      title_only_items = (all_items - items).select &:title_is_public?
    else

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

Open

  def create
    if handle_upload_data
      @model = Model.new(params[:model])

      @model.policy.set_attributes_with_sharing params[:sharing], @model.projects

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

Open

  def existing_specimens
    specimens_of_strains = []
    strains = []
    specimens_with_default_strain =[]
    if params[:strain_ids]

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

Open

  def preview_permissions
      policy = sharing_params_to_policy
      current_person = User.current_user.try(:person)
      contributor_person = (params['is_new_file'] == 'false') ?  User.find_by_id(params['contributor_id'].to_i).try(:person) : current_person
      creators = (params["creators"].blank? ? [] : ActiveSupport::JSON.decode(params["creators"])).uniq

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

Open

  def resource_in_tab
    resource_type = params[:resource_type]
    view_type = params[:view_type]
    scale_title = params[:scale_title] || ''

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

Open

      def self.included klass
        klass.class_eval do
          searchable do
            text :title do
              if self.respond_to?(:title)

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

Open

    def populate      
      begin
        @translucent_id = @node.find_first("id").content unless @node.find_first("id").nil?
        @author_seek_id = @node.find_first("submitter").content unless @node.find_first("submitter").nil?
        if @type=="Model"

Similar blocks of code found in 2 locations. Consider refactoring.

Open

            slider.maxThreshold = (slider.settings.maxSlides * slider.settings.slideWidth) + ((slider.settings.maxSlides - 1) * slider.settings.slideMargin);

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

            slider.minThreshold = (slider.settings.minSlides * slider.settings.slideWidth) + ((slider.settings.minSlides - 1) * slider.settings.slideMargin);

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    if cls.nil?
      flash.now[:error] = "Unrecognised assay type"
    elsif !params[:label].blank? && params[:label].downcase != cls.label.downcase
      flash.now[:notice] = "Undefined assay type with label <b> #{params[:label]} </b>. Did you mean #{view_context.link_to(cls.label, assay_types_path(:uri=>uri, :label=> cls.label),{:style=> "font-style:italic;font-weight:bold;"})}?".html_safe
    else

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