Function roundRectangleIntersectLine has 97 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    canvas_prototype.roundRectangleIntersectLine = function(
        x, y, nodeX, nodeY, width, height, padding) {

        //Manually change for seek to fix that safari quits unexpectedly
        var cornerRadius = 0;

Method add_as_new has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.

Open

    def add_as_new resource
      #FIXME: this method is too long 
      begin
        warning=nil
        warning_code=0

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Method build_all_bio_sample_json has 92 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def build_all_bio_sample_json sheet

      # population order should NOT change, DB is populated only if @to_populate is set to be true

      # probing number of rows with data in sheet

Method text_or_not_specified has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

  def text_or_not_specified text, options = {}
    text=text.to_s if text.kind_of?(Numeric)
    if text.nil? or text.chomp.empty?
      not_specified_text||=options[:none_text]
      not_specified_text||="No description specified" if options[:description]==true

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Method handle_upload_data has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

      def handle_upload_data
        blob_params = content_blob_params

        # MERGENOTE - the manipulation and validation of the params still needs a bit of cleaning up
        blob_params = update_params_for_batch(blob_params)

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Method generate_triples has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

      def generate_triples subject, method, property,uri_or_literal,transformation,collection_transform,rdf_graph
        resource = subject.rdf_resource
        transform = transformation.strip unless transformation.nil?
        collection_transform = collection_transform.strip unless collection_transform.nil?
        items = subject.send(method)

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Method populate_specimen has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

    def populate_specimen specimen_json

      specimen_title = specimen_json["title"]
      sex = specimen_json["sex"]
      age = specimen_json["age"]

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Method populate_treatment has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

    def populate_treatment treatment_json, specimen=nil, sample=nil

        start_value = treatment_json["start value"]
        end_value = treatment_json["end value"]
        standard_deviation = treatment_json["standard deviation"]

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Function dragObject has 89 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function dragObject(element, attachElement, lowerBound, upperBound, startCallback, moveCallback, endCallback, attachLater)
{
  if(typeof(element) == "string")
    element = document.getElementById(element);
  if(element == null)

Function dragObject has 89 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function dragObject(element, attachElement, lowerBound, upperBound, startCallback, moveCallback, endCallback, attachLater)
{
  if(typeof(element) == "string")
    element = document.getElementById(element);
  if(element == null)

File data_files_controller.rb has 313 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'simple-spreadsheet-extractor'

class DataFilesController < ApplicationController

  include IndexPager

Method populate_specimen has 86 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def populate_specimen specimen_json

      specimen_title = specimen_json["title"]
      sex = specimen_json["sex"]
      age = specimen_json["age"]

Method parse_spreadsheet_xml has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.

Open

      def parse_spreadsheet_xml(spreadsheet_xml)
        workbook = Workbook.new

        doc = LibXML::XML::Parser.string(spreadsheet_xml).parse
        doc.root.namespaces.default_prefix="ss"

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Method populate has a Cognitive Complexity of 24 (exceeds 5 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"

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Class Publication has 28 methods (exceeds 20 allowed). Consider refactoring.

Open

class Publication < ActiveRecord::Base
  include Seek::Rdf::RdfGeneration
  title_trimmer
  alias_attribute :description, :abstract
  #searchable must come before acts_as_asset is called

Class Workflow has 28 methods (exceeds 20 allowed). Consider refactoring.

Open

class Workflow < ActiveRecord::Base

  acts_as_asset

  scope :default_order, order('title')

Class ModelsController has 28 methods (exceeds 20 allowed). Consider refactoring.

Open

class ModelsController < ApplicationController

  include WhiteListHelper
  include IndexPager
  include DotGenerator

Method add_items_to_queue has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

  def self.add_items_to_queue items, t=5.seconds.from_now, priority=0, queuepriority=priority
    if Seek::Config.auth_lookup_enabled

      items = [items] if items.nil?
      items = Array(items)

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Function prototype has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

Search.prototype = $.extend({}, Navigation, new function() {
  var suid = 1;

  this.init = function() {
    var _this = this;

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Method authorized_list has a Cognitive Complexity of 23 (exceeds 5 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

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