SysMO-DB/seek

Method create has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    if handle_upload_data
      @presentation = Presentation.new(params[:presentation])

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

Method edit_tag has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def edit_tag
    if request.post?
      @tag=TextValue.find(params[:id])
      replacement_tags = []

Method create has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    @publication = Publication.new(params[:publication])
    @publication.pubmed_id=nil if @publication.pubmed_id.blank?
    @publication.doi=nil if @publication.doi.blank?
    pubmed_id,doi = preprocess_doi_or_pubmed @publication.pubmed_id,@publication.doi

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

Open

      case 40: //Event.KEY_DOWN:
        if (e.keyCode == 40 || e.ctrlKey) {
          if (this.moveDown()) e.preventDefault();
          this.startMoveTimeout(true);
        }

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

Open

      case 38: //Event.KEY_UP:
        if (e.keyCode == 38 || e.ctrlKey) {
          if (this.moveUp()) e.preventDefault();
          this.startMoveTimeout(false);
        }

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Consider simplifying this complex logical expression.

Open

          unless sample.specimen == specimen &&
              sample.sample_type == sample_type &&
              (sample.tissue_and_cell_types.member?(tissue_and_cell_type) || tissue_and_cell_type_title == "") &&
              sample.donation_date == Time.zone.parse(donation_date).utc &&
              sample.institution == institution &&

Function validateResourceFields has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function validateResourceFields(is_new_file, resource_name, is_managed) {
    // check if sharing rights are defined
    if (!($(document.getElementById('sharing_scope_0')).checked) &&
        !($(document.getElementById('sharing_scope_2')).checked) &&
        !($(document.getElementById('sharing_scope_4')).checked))

Function init has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var init = function(){
            // merge user-supplied options with the defaults
            slider.settings = $.extend({}, defaults, options);
            // parse slideWidth setting
            slider.settings.slideWidth = parseInt(slider.settings.slideWidth);

Method list_samples_and_assay_organisms has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def list_samples_and_assay_organisms attribute, assay_samples, assay_organisms, html_options={}, none_text="Not Specified"

    result= "<p class='#{html_options[:class]}' id='#{html_options[:id]}'> <b>#{attribute}</b>: "

    result +="<span class='none_text'>#{none_text}</span>" if assay_samples.blank? and assay_organisms.blank?

Method cytoscape_node_elements has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def cytoscape_node_elements nodes
    cytoscape_node_elements = []
    nodes.each do |node|
      item_type, item_id = node.split('_')
      item = item_type.constantize.find_by_id(item_id)

Method update has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def update
    data_file_ids = (params[:sample_data_file_ids].nil? ? [] : params[:sample_data_file_ids].reject(&:blank?)) || []
    model_ids = (params[:sample_model_ids].nil? ? [] : params[:sample_model_ids].reject(&:blank?)) || []
    sop_ids = (params[:sample_sop_ids].nil? ? [] : params[:sample_sop_ids].reject(&:blank?)) || []
    @sample.attributes = params[:sample]

Method paginate_after_fetch has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def paginate_after_fetch(collection, *args)
      options=args.pop unless args.nil?
      options ||= {}
      reorder = options[:reorder].nil? ? true : options[:reorder]

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

Open

        var clickNextBind = function(e){
            // if auto show is running, stop it
            if (slider.settings.auto) el.stopAuto();
            el.goToNextSlide();
            e.preventDefault();

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

Open

        var clickPrevBind = function(e){
            // if auto show is running, stop it
            if (slider.settings.auto) el.stopAuto();
            el.goToPrevSlide();
            e.preventDefault();

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

Open

if(document.form.plotGraphPanel.checked==true) {
    rc.SetCurrentWidth2(cookieToArray('rc')[0]);
    rc.SetCurrentHeight(cookieToArray('rc')[1]);
    };

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

Open

if(document.form.plotKineticsPanel.checked==true) {rc2.SetCurrentWidth2(cookieToArray('rc2')[0]);rc2.SetCurrentHeight(cookieToArray('rc2')[1]);};

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Function onTouchEnd has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var onTouchEnd = function(e){
            slider.viewport.unbind('touchmove', onTouchMove);
            var orig = e.originalEvent;
            var value = 0;
            // record end x, y positions

Function getViewportHeight has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        var getViewportHeight = function(){
            var height = 0;
            // first determine which children (slides) should be used in our height calculation
            var children = $();
            // if mode is not "vertical" and adaptiveHeight is false, include all children

Function updateEvents has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateEvents() {
    event_text = '<ul class="related_asset_list">'
    for (var i = 0; i < events_array.length; i++) {
        var event = events_array[i];
        var title = event[0];

Method set_attributes_with_sharing has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def set_attributes_with_sharing sharing, projects
    # if no data about sharing is given, it should be some user (not the owner!)
    # who is editing the asset - no need to do anything with policy / permissions: return success
    self.tap do |policy|
      if sharing