Method make_lat_long_matching_table has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

  def make_lat_long_matching_table(*pieces, collection)
    columns = ['CEID', 'Match', 'Verbatim Lat', 'Verbatim Long',
               'Decimal lat', 'Decimal long', 'Is georeferenced?', 'Select']

    thead = content_tag(:thead) do

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Method otu has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    def otu(columns)
      r = BatchLoad::ColumnResolver::Result.new

      if columns['otu_id']
        begin

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Method autocomplete has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

      def autocomplete
        return [] if query_string.blank? || project_id.empty?

        queries = [
          [ autocomplete_exact_id, false ],

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Method build_asserted_distributions has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    def build_asserted_distributions
      i = 1
      csv.each do |row|
        i += 1

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Method build_sequences has 64 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def build_sequences
      @total_data_lines = 0;

      sequences = {}
      sequence_values = {}

Method generate has 64 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def self.generate(otus, project_members, root_otu_id = nil, reference_csv = nil, prefer_unlabelled_otus: true)

    # Until we have RC5 articulations we are simplifying handling the fact
    # that one taxon name can be used for many OTUs. Track to see that
    # an OTU with a given taxon name does not already exist

File draw.js has 272 lines of code (exceeds 250 allowed). Consider refactoring.

Open

/*
 * extended library to construct drawable Google map instances
 */
var TW = TW || {};                      // TW "namespacing" object
TW.vendor = TW.vendor || {};            // mimic directory structure in app/assets/javascripts

Class DataAttributesController has 23 methods (exceeds 20 allowed). Consider refactoring.

Open

class DataAttributesController < ApplicationController
  include DataControllerConfiguration::ProjectDataControllerConfiguration

  before_action :set_data_attribute, only: [:update, :destroy, :api_show]
  after_action -> { set_pagination_headers(:data_attributes) }, only: [:index, :api_index ], if: :json_request?

Function default has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

export default function (state, observation) {
  if (!observation.type) { throw `Observations must have a type!` }

  if (Object.keys(ObservationTypes).findIndex(typeKey => ObservationTypes[typeKey] === observation.type) === -1) { throw `Observations must have a valid type! Given ${observation.type}` }

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Function initializeDrawingManager has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    initializeDrawingManager: function (map, mapDrawingModes) {
      var drawingMode = undefined;      // "active: circle, polygon, circle" results in hand, polygon, circle(selected)
      var drawingModes = [];            // "polygon, circle" results in hand(active), polygon, circle in draw mode menu
      var i;                  // loop counter
      var j = 0;              // offset for start of i-loop when ACTIVE:mode has explicit position

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Method sv_single_sub_taxon has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def sv_single_sub_taxon
      if self.rank_class
        rank = rank_string
        if rank != 'potentially_validating rank' && self.rank_class.nomenclatural_code == :iczn && %w(subspecies subgenus subtribe tribe subfamily).include?(self.rank_class.rank_name)
          sisters = self.parent.descendants.with_rank_class(rank).select{|t| t.id == t.cached_valid_taxon_name_id}

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Method sv_species_gender_agreement_not_required has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def sv_species_gender_agreement_not_required
      if is_species_rank? && ((!feminine_name.blank? || !masculine_name.blank? || !neuter_name.blank?)) && is_available?
        s = part_of_speech_name
        if !s.nil? && !%w{adjective participle}.include?(s)
          soft_validations.add(:feminine_name, 'Alternative spelling is not required for the name which is not adjective or participle.') unless feminine_name.blank?

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Method sources_autocomplete_tag has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

  def sources_autocomplete_tag(source, term)
    return nil if source.nil?

    if term
      s = regex_mark_tag(source.cached, term) + ' '

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Method geographic_area has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def geographic_area(columns, data_origin = nil)
      r = BatchLoad::ColumnResolver::Result.new

      if columns['geographic_area_id']
        begin

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Method create has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def create
      sorted_processed_rows.each_value do |processed_row|
        otu = processed_row.objects[:otu].first
        d_a = processed_row.objects[:data_attribute].first
        cvt = processed_row.objects[:predicate].first

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Method data_for has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

  def self.data_for(collection_object)
    o = collection_object
    data = Catalog::CollectionObject::Entry.new(o)

    data.items << Catalog::CollectionObject::EntryItem.new(type: :collected_on, object: o.collecting_event, start_date: o.collecting_event.start_date, end_date: o.collecting_event.end_date) if o.collecting_event_id.present?

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Method get_bibtex_string has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def self.get_bibtex_string(citation, format = 'bibtex')
      begin
        # Convert citation to DOI if it isn't already
        if !citation_is_valid_doi?(citation)
          # First item should be the one with highest score/relevance: https://github.com/CrossRef/rest-api-doc#sort-order

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Method using_isbn_class has 59 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def using_isbn_class
    unless identifier.nil?
      isbn = identifier.upcase
      # 'ISBN-13: 978-0-596-52068-7'
      isbn.gsub!('ISBN-10', '')

Method all_sub_headers has 59 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def all_sub_headers(filtered = false)
    unless filtered
      ce_headers # generate the header structure (see CollectionObject.selected_column_names)
      co_headers
      bc_headers

Method taxonworks_extension_data has 59 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def taxonworks_extension_data
      return @taxonworks_extension_data if @taxonworks_extension_data

      # hash of internal method name => csv header name
      methods = {}