Method extract_species_and_reaction_names has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

      def extract_species_and_reaction_names doc
        species = []
        reactions = []
        species_names_node = doc.find_first("//speciesNames")
        species_names_node.children.each do |child|

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Method authorized_associations_for_action? has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

        def authorized_associations_for_action?
          result = true
          if self.class.respond_to?(:associations_and_actions_to_be_enforced)
            self.class.associations_and_actions_to_be_enforced.keys.each do |association|
              if self.respond_to?(association)

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Function tab_on_click has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function tab_on_click(scale_title, resource_type, resource_ids, actions_partial_disable){
    var click_tab = document.getElementsByClassName(scale_title + '_' + resource_type)[0];
    click_tab.onclick = function(){
        deactivate_previous_tab(this);
        click_tab.parentElement.className = 'tabberactive';

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

Open

  def summarize_permissions creators=[User.current_user.try(:person)], asset_managers = [], contributor=User.current_user.try(:person)
        #build the hash containing contributor_type as key and the people in these groups as value,exception:'Public' holds the access_type as the value
        people_in_group = {'Person' => [], 'FavouriteGroup' => [], 'WorkGroup' => [], 'Project' => [], 'Institution' => [], 'WhiteList' => [], 'BlackList' => [],'Network' => [], 'Public' => 0}
        #the result return: a hash contain the access_type as key, and array of people as value
        grouped_people_by_access_type = {}

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

Open

  def list_item_visibility item,css_class="visibility_icon"
    title = ""
    html  = ""
    policy = item.policy

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

Open

  def model_scales_list model, list_item
    scales = model.scales
    if scales.empty?
      text_or_not_specified("")
    else

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

Open

  def matching_data_files params_only=false
    
    results = {}

    if Seek::Config.solr_enabled && is_jws_supported?

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

Open

  def create_from_existing
    studied_factor_ids = []
    new_studied_factors = []
    #retrieve the selected FSes

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

Open

  def create
    content = params[:annotation_content].strip
    if !content.blank?
      worksheet = @content_blob.worksheets.select {|w| w.sheet_number == params[:annotation_sheet_id].to_i}.first

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'

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] || ''