Method fetch_preview has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def fetch_preview
    #trim the PubMed or Doi Id
    params[:key] = params[:key].strip() unless params[:key].blank?
    params[:publication][:project_ids].reject!(&:blank?).map! { |id| id.split(',') }.flatten!
    @publication = Publication.new(params[:publication])

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Method update_others has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def update_others
    update_flag = true
    if Seek::Config.tag_threshold.to_s != params[:tag_threshold] || Seek::Config.max_visible_tags.to_s!=params[:max_visible_tags]
      expire_annotation_fragments
    end

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Method show has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def show
    respond_to do |format|
      format.html do
        # see notes in application.rb on how this works
        update_last_seen_at

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Method duesseldorf_bode_surgical_mapping has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def duesseldorf_bode_surgical_mapping

      gene_modification_regex = /([\w\d]+)([\/+-]+)/

      {

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Method filter_size has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

      def filter_size size
        size = size[0..-($1.length.to_i + 2)] if size =~ /[0-9]+x[0-9]+\.([a-z0-9]+)/ # trim file extension
        max_size=MAX_SIZE
        matches = size.match /([0-9]+)x([0-9]+).*/
        if matches

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Method update_substance has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def update_substance(substance)
    unless substance.blank?
         #call the webservice to retrieve the substance annotation from sabiork
         #the annotation is stored in a hash, which keys: recommended_name, synonyms, sabiork_id, chebi_ids, kegg_ids
         compound_annotation = Seek::SabiorkWebservices.new().get_compound_annotation(substance)

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Method update has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:presentation]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:presentation].delete(column_name)

Method open_id_authentication has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def open_id_authentication(identity_url)
    # Pass optional :required and :optional keys to specify what sreg fields you want.
    # Be sure to yield registration, a third argument in the #authenticate_with_open_id block.
    authenticate_with_open_id(identity_url,        
        :required => [:email, :fullname,

Method update has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:model]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:model].delete(column_name)

Method insert_results has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def insert_results
    resources=[]
    @project=Project.find(params[:project])
    params.keys.each do |key|
      if key.start_with?("title")

Function performSearch has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function performSearch(data, regexps, queries, highlighters, state) {
    var searchIndex = data.searchIndex;
    var longSearchIndex = data.longSearchIndex;
    var info = data.info;
    var result = [];

Method create has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @topic = Topic.find_by_id_and_forum_id(params[:topic_id],params[:forum_id])
    if @topic.locked?
      respond_to do |format|
        format.html do

Method search_in_sabiork has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def search_in_sabiork
     unless params[:compound_name].blank?
       compound_annotation = Seek::SabiorkWebservices.new().get_compound_annotation(params[:compound_name])
       unless compound_annotation.blank?
           synonyms = compound_annotation['synonyms'].inject{|result, s| result.concat("; #{s}")}

Method update has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def update
        raise Exception.new("No ID") if seek_id.blank?
        person_record=Person.find_by_id(seek_id)
        raise Exception.new("Unable to find person with ID: #{seek_id}") if person_record.nil?
        raise Exception.new("Person is not a member of Translucent") unless person_record.projects.include?(@project)  

Method menu_definitions has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def menu_definitions
    definitions=[
        {:title=>t("menu.yellow_pages"), :sections=>[
            {:controller=>"programmes",:title=>t('programme').pluralize,:hide=>!Seek::Config.programmes_enabled},
            {:controller=>"people",:title=>"People"},

Method runs_table has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def runs_table(runs, redirect_to=nil)
    runs.map do |run|
      workflow = run.workflow
      version = run.workflow_version
      workflow_version = workflow.find_version(version)

Method update has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:sop]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:sop].delete(column_name)

Method associate_authors has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def associate_authors
    publication = @publication
    projects = publication.projects
    projects = current_user.person.projects if projects.empty?
    association = {}

Function setPositionProperty has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var setPositionProperty = function(value, type, duration, params){
            // use CSS transform
            if(slider.usingCSS){
                // determine the translate3d value
                var propValue = slider.settings.mode == 'vertical' ? 'translate3d(0, ' + value + 'px, 0)' : 'translate3d(' + value + 'px, 0, 0)';

Function generate_json_data has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function generate_json_data() {
    var cells = $j('td.selected_cell');
    var columns = $j('.col_heading.selected_heading').size();
    var headings;
    var rows = new Array();