Module: Abstractor::Methods::Models::AbstractorSubject::InstanceMethods

Included in:
AbstractorSubject
Defined in:
lib/abstractor/methods/models/abstractor_subject.rb

Instance Method Summary collapse

Instance Method Details

#abstract(about) ⇒ void

This method returns an undefined value.

Creates or finds an instance of an Abstractor::AbstractorAbstraction. The method will create instances of Abstractor::AbstractorSuggestion and Abstractor::AbstractorSuggestionSource for the abstractable entity passed via the about parameter.

The method cycles through each Abstractor::AbstractorAbstractionSource setup for the instance of the Abstractor::AbstractorSubject. The Abstractor::AbstractorSubject#abstractor_abstraction_source_type attribute determines the abstraction strategy:

  • ‘nlp suggestion’: creates instances of Abstractor::AbstractorSuggestion based on natural language processing (nlp) logic searching the text provided by the Abstractor::AbstractorSubject#from_methd attribute.

  • ‘custom suggestion’: creates instances of Abstractor::AbstractorSuggestion based on custom logic delegated to the method configured in AbstractorAbstractionSource#custom_method.

  • ‘indirect’: creates an instance of Abstractor::AbstractorIndirectSource wih null source_type, source_id, source_method attributes – all waiting to be set upon selection of an indirect source.

  • ‘custom nlp suggestion’: looks up a suggestion endpoint to submit text, object values and object value variants to an external, custom NLP provider for the delegation of suggestion generation.

Parameters:

  • about (ActiveRecord::Base) —

    The entity to abstract. An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 45

def abstract(about)
  abstractor_abstraction = about.find_or_create_abstractor_abstraction(abstractor_abstraction_schema, self)

  abstractor_abstraction_sources.each do |abstractor_abstraction_source|
    case abstractor_abstraction_source.abstractor_abstraction_source_type.name
    when 'nlp suggestion'
      abstract_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
    when 'custom suggestion'
      abstract_custom_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
    when 'indirect'
      abstract_indirect_source(about, abstractor_abstraction, abstractor_abstraction_source)
    when 'custom nlp suggestion'
      abstract_custom_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
    end
  end
end

#abstract_canonical_name_value(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 248

def abstract_canonical_name_value(about, abstractor_abstraction, abstractor_abstraction_source)
  abstractor_abstraction_source.normalize_from_method_to_sources(about).each do |source|
    abstractor_text = Abstractor::AbstractorAbstractionSource.abstractor_text(source)
    parser = Abstractor::Parser.new(abstractor_text)
    abstractor_abstraction_schema.predicate_variants.each do |predicate_variant|
      abstractor_abstraction_schema.abstractor_object_values.each do |abstractor_object_value|
        abstractor_object_value.object_variants.each do |object_variant|
          match_value = "#{Regexp.escape(predicate_variant)}:\s*#{Regexp.escape(object_variant)}"
          matches = parser.scan(match_value, word_boundary: true).uniq
          matches.each do |match|
            suggest(abstractor_abstraction, abstractor_abstraction_source, match, match, source[:source_id], source[:source_type].to_s, source[:source_method], source[:section_name],  abstractor_object_value, nil, nil, nil, nil)
          end

          match_value = "#{Regexp.escape(predicate_variant)}#{Regexp.escape(object_variant)}"
          matches = parser.scan(match_value, word_boundary: true).uniq
          matches.each do |match|
            suggest(abstractor_abstraction, abstractor_abstraction_source, match, match, source[:source_id], source[:source_type].to_s, source[:source_method], source[:seciton_name], abstractor_object_value, nil, nil, nil, nil)
          end
        end
      end
    end
  end
end

#abstract_custom_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ void

This method returns an undefined value.

Looks up a suggestion endpoint to submit text to an external custom NLP provider for the delegation of suggestion generation.

The method will determine an endpoint by looking in config/abstractor/custom_nlp_providers.yml based on the current environment and the value of the AbstractorAbstractionSource#custom_nlp_provider attribute.

A template configratuon file can be generated in the the host application by calling the rake task abstractor:custom_nlp_provider. The configuration is expected to provide different endpoints per environment, per provider. Abstractor will format a JSON body to post to the discovered endpoint. The custom NLP provider will be expected to generate suggestions and post them back to /abstractor_abstractions/:abstractor_abstraction_id/abstractor_suggestions/

Examples:

Example of body prepared by Abstractor to submit to an custom NLP provider

{
  "abstractor_abstraction_schema_id":1,
  "abstractor_abstraction_schema_uri":"https://moomin.com/abstractor_abstraction_schemas/1",
  "abstractor_abstraction_id":1,
  "abstractor_abstraction_source_id":1,
  "source_type":  "PathologyCase",
  "source_method": "note_text",
  "text": "The patient has a diagnosis of glioblastoma.  GBM does not have a good prognosis.  But I can't rule out meningioma."
}

Parameters:

  • about (ActiveRecord::Base) —

    The entity to abstract. An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.

  • abstractor_abstraction (Abstractor::AbstractorAbstraction) —

    The instance of Abstractor::AbstractorAbstraction to make suggestions against.

  • abstractor_abstraction_source (Abstractor::AbstractorAbstractionSource) —

    The instance of the Abstractor::AbstractorAbstractionSource that provides the name of the custom NLP provider.



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 169

def abstract_custom_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
  suggestion_endpoint = CustomNlpProvider.determine_suggestion_endpoint(abstractor_abstraction_source.custom_nlp_provider)
  abstractor_abstraction_source.normalize_from_method_to_sources(about).each do |source|
    abstractor_text = Abstractor::AbstractorAbstractionSource.abstractor_text(source)
    body = Abstractor::CustomNlpProvider.format_body_for_suggestion_endpoint(abstractor_abstraction, abstractor_abstraction_source, abstractor_text, source)
    HTTParty.post(suggestion_endpoint, body: body.to_json, headers: { 'Content-Type' => 'application/json' })
  end
end

#abstract_custom_suggestion(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ void

This method returns an undefined value.

Creates instances of Abstractor::AbstractorSuggestion and Abstractor::AbstractorSuggestionSource based on calling the method configured by the AbstractorAbstractionSource#custom_method attribute. The method is called on the abstractable entity passed via the about parameter.

Setting up an Abstractor::AbstractorSubject with an AbstractorAbstractionSource with an AbstractorAbstractionSource#abstractor_abstraction_source_type attribute set to ‘custom suggestion’ obligates the developer to implement an instance method on the abstractable entitty to make suggestions as appropriate. The ‘custom suggestion’ source type is intended to faciliate the generation of suggestions in a customizable way. The method implemented by the developer should return an array of hashes, each has with 2 keys, like so

{ suggestion: ‘a suggestion’, explanation: ‘why i made the suggestion}

The suggestion will be presented to the user as possible answer for the abstraction. The explanation will be displayed to the user to explain how the sytem arrived at the suggestion.

Parameters:

  • about (ActiveRecord::Base) —

    The entity to abstract. An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.

  • abstractor_abstraction (Abstractor::AbstractorAbstraction) —

    The instance of Abstractor::AbstractorAbstraction to make suggestions against.

  • abstractor_abstraction_source (Abstractor::AbstractorAbstractionSource) —

    The instance of the Abstractor::AbstractorAbstractionSource that provides the custom method to invoke on the abstractable entity to make custom suggestions.



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 133

def abstract_custom_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
  suggestions = about.send(abstractor_abstraction_source.custom_method, abstractor_abstraction)
  suggestions.each do |suggestion|
    suggest(abstractor_abstraction, abstractor_abstraction_source, nil, nil, about.id, about.class.to_s, abstractor_abstraction_source.from_method, abstractor_abstraction_source.section_name, suggestion[:suggestion], nil, nil, abstractor_abstraction_source.custom_method, suggestion[:explanation])
  end
  create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
end

#abstract_indirect_source(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ void

This method returns an undefined value.

Creates an instance of Abstractor::AbstractorIndirectSource – if one does not already exist – for the abstractor_abstraction and abstraction_source parameters. An ‘indirect’ Abstractor::AbstractorAbstractionSources give developers the ability to define a pool of documents that are indrectly related to an abstraction. The developer is responsible for implementing a method on the abstractable enttiy specified in Abstractor::AbstractorAbstractionSource#from_method. The method should return a hash with the following keys populated:

  • Array <ActiveRecord::Base>

    :sources An array of active record objects that constitute the list of indirect sources.

  • Symbol

    :source_id A method specifying the primary key of each member in sources.

  • Symbol

    :source_method A method specifying the source text of each member in sources.

Parameters:

  • about (ActiveRecord::Base) —

    The entity to abstract. An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.

  • abstractor_abstraction (Abstractor::AbstractorAbstraction) —

    The instance of Abstractor::AbstractorAbstraction to insert an indirect source.

  • abstractor_abstraction_source (Abstractor::AbstractorAbstractionSource) —

    The instance of the Abstractor::AbstractorAbstractionSource that provides the indirec source.



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 79

def abstract_indirect_source(about, abstractor_abstraction, abstractor_abstraction_source)
  if !abstractor_abstraction.detect_abstractor_indirect_source(abstractor_abstraction_source)
    source = about.send(abstractor_abstraction_source.from_method)
    abstractor_abstraction.abstractor_indirect_sources.build(abstractor_abstraction_source: abstractor_abstraction_source, source_type: source[:source_type], source_method: source[:source_method])
    abstractor_abstraction.save!
  end
end

#abstract_name_value(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 241

def abstract_name_value(about, abstractor_abstraction, abstractor_abstraction_source)
  abstract_canonical_name_value(about, abstractor_abstraction, abstractor_abstraction_source)
  abstract_sentential_name_value(about, abstractor_abstraction, abstractor_abstraction_source)
  create_unknown_abstractor_suggestion_name_only(about, abstractor_abstraction, abstractor_abstraction_source)
  create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
end

#abstract_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ void

This method returns an undefined value.

Creates instances of Abstractor::AbstractorSuggestion and Abstractor::AbstractorSuggestionSource based on natural languange processing (nlp).

The Abstractor::AbstractorSubject#abstractor_rule_type attribute determines the nlp strategy to employ:

  • ‘name/value’: attempts to search for non-negated sentences mentioning of an Abstractor::AbstractorAbstractionSchema#predicate and an Abstractor::AbstractorObjectValue

  • ‘value’: attempts to search for non-negated sentences mentioning an Abstractor::AbstractorObjectValue

  • ‘unknown’: will automatically create an ‘unknown’ Abstractor::AbstractorSuggestion

Parameters:

  • about (ActiveRecord::Base) —

    The entity to abstract. An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.

  • abstractor_abstraction (Abstractor::AbstractorAbstraction) —

    The instance of Abstractor::AbstractorAbstraction to make suggestions against.

  • abstractor_abstraction_source (Abstractor::AbstractorAbstractionSource) —

    The instance of the Abstractor::AbstractorAbstractionSource that provides the rule type and from method to make nlp suggestions.



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 101

def abstract_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
  case abstractor_abstraction_source.abstractor_rule_type.name
  when 'name/value'
    abstract_name_value(about, abstractor_abstraction, abstractor_abstraction_source)
  when 'value'
    abstract_value(about, abstractor_abstraction, abstractor_abstraction_source)
  when 'unknown'
    abstract_unknown(about, abstractor_abstraction, abstractor_abstraction_source)
  end
end

#abstract_sentential_name_value(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 272

def abstract_sentential_name_value(about, abstractor_abstraction, abstractor_abstraction_source)
  abstractor_abstraction_source.normalize_from_method_to_sources(about).each do |source|
    abstractor_text = Abstractor::AbstractorAbstractionSource.abstractor_text(source)
    parser = Abstractor::Parser.new(abstractor_text)
    abstractor_abstraction_schema.predicate_variants.each do |predicate_variant|
      ranges = parser.range_all(Regexp.escape(predicate_variant))
      if ranges.any?
        ranges.each do |range|
          sentence = parser.find_sentence(range)
          if sentence
            abstractor_abstraction_schema.abstractor_object_values.each do |abstractor_object_value|
              abstractor_object_value.object_variants.each do |object_variant|
                match = parser.match_sentence(sentence[:sentence], Regexp.escape(object_variant))
                if match
                  scoped_sentence = Abstractor::NegationDetection.parse_negation_scope(sentence[:sentence])
                  reject = (
                             Abstractor::NegationDetection.negated_match_value?(scoped_sentence[:scoped_sentence], predicate_variant) ||
                             Abstractor::NegationDetection.manual_negated_match_value?(sentence[:sentence], predicate_variant) ||
                             Abstractor::NegationDetection.negated_match_value?(scoped_sentence[:scoped_sentence], object_variant) ||
                             Abstractor::NegationDetection.manual_negated_match_value?(sentence[:sentence], object_variant)
                           )
                  if !reject
                    suggest(abstractor_abstraction, abstractor_abstraction_source, sentence[:sentence], sentence[:sentence], source[:source_id], source[:source_type].to_s, source[:source_method], source[:section_name], abstractor_object_value, nil, nil, nil, nil)
                  end
                end
              end
            end
          end
        end
      end
    end
  end
end

#abstract_sentential_value(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 187

def abstract_sentential_value(about, abstractor_abstraction, abstractor_abstraction_source)
  abstractor_abstraction_source.normalize_from_method_to_sources(about).each do |source|
    abstractor_text = Abstractor::AbstractorAbstractionSource.abstractor_text(source)
    abstractor_object_value_ids = abstractor_abstraction_schema.abstractor_object_values.map(&:id)

    abstractor_object_values = []
    abstractor_object_value_variants = []
    target_abstractor_object_values =[]
    target_abstractor_object_value_variants = Abstractor::AbstractorObjectValueVariant.where("abstractor_object_value_id in (?)", abstractor_object_value_ids).to_a

    at = nil
    at = abstractor_text.downcase unless abstractor_text.blank?
    target_abstractor_object_value_variants.each do |abstractor_object_value_variant|
      re = Regexp.new('\b' + Regexp.escape(abstractor_object_value_variant.value.downcase) + '\b')
      if re =~ at
        abstractor_object_value_variants << abstractor_object_value_variant
        abstractor_object_values << abstractor_object_value_variant.abstractor_object_value
      end
    end

    target_abstractor_object_values = abstractor_abstraction_schema.abstractor_object_values
    target_abstractor_object_values = target_abstractor_object_values - abstractor_object_values

    target_abstractor_object_values.each do |abstractor_object_value|
      re = Regexp.new('\b' + Regexp.escape(abstractor_object_value.value.downcase) + '\b')
      if re =~ at
        abstractor_object_values << abstractor_object_value
      end
    end

    parser = Abstractor::Parser.new(abstractor_text)
    abstractor_object_values.each do |abstractor_object_value|
      object_variants(abstractor_object_value, abstractor_object_value_variants).each do |object_variant|
        ranges = parser.range_all(Regexp.escape(object_variant.downcase))
        if ranges.any?
          ranges.each do |range|
            sentence = parser.find_sentence(range)
            if sentence
              scoped_sentence = Abstractor::NegationDetection.parse_negation_scope(sentence[:sentence])
              reject = (
                        Abstractor::NegationDetection.negated_match_value?(scoped_sentence[:scoped_sentence], object_variant) ||
                        Abstractor::NegationDetection.manual_negated_match_value?(sentence[:sentence], object_variant)
                      )
              if !reject
                suggest(abstractor_abstraction, abstractor_abstraction_source, object_variant.downcase, sentence[:sentence], source[:source_id], source[:source_type].to_s, source[:source_method], source[:section_name], abstractor_object_value, nil, nil, nil, nil)
              end
            end
          end
        end
      end
    end
  end
end

#abstract_unknown(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 178

def abstract_unknown(about, abstractor_abstraction, abstractor_abstraction_source)
  create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
end

#abstract_value(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 182

def abstract_value(about, abstractor_abstraction, abstractor_abstraction_source)
  abstract_sentential_value(about, abstractor_abstraction, abstractor_abstraction_source)
  create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
end

#abstractor_object_value?(suggested_value) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 345

def abstractor_object_value?(suggested_value)
  suggested_value.instance_of?(Abstractor::AbstractorObjectValue)
end

#create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 377

def create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
  #Create an 'unknown' suggestion based on matching nothing only if we have not made a suggstion
  abstractor_abstraction_source.normalize_from_method_to_sources(about).each do |source|
    if abstractor_abstraction.abstractor_suggestions(true).select { |abstractor_suggestion| abstractor_suggestion.unknown != true }.empty?
      suggest(abstractor_abstraction, abstractor_abstraction_source, nil, nil, source[:source_id], source[:source_type].to_s, source[:source_method],source[:section_name],  nil, true, nil, nil, nil)
    end
  end
end

#create_unknown_abstractor_suggestion_name_only(about, abstractor_abstraction, abstractor_abstraction_source) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 349

def create_unknown_abstractor_suggestion_name_only(about, abstractor_abstraction, abstractor_abstraction_source)
  abstractor_abstraction_source.normalize_from_method_to_sources(about).each do |source|
    abstractor_text = Abstractor::AbstractorAbstractionSource.abstractor_text(source)
    parser = Abstractor::Parser.new(abstractor_text)
    #Create an 'unknown' suggestion based on match name only if we have not made a suggstion
    if abstractor_abstraction.abstractor_suggestions(true).empty?
      abstractor_abstraction_schema.predicate_variants.each do |predicate_variant|
        ranges = parser.range_all(Regexp.escape(predicate_variant))
        if ranges
          ranges.each do |range|
            sentence = parser.find_sentence(range)
            if sentence
              scoped_sentence = Abstractor::NegationDetection.parse_negation_scope(sentence[:sentence])
              reject = (
                        Abstractor::NegationDetection.negated_match_value?(scoped_sentence[:scoped_sentence], predicate_variant) ||
                        Abstractor::NegationDetection.manual_negated_match_value?(sentence[:sentence], predicate_variant)
                      )
              if !reject
                suggest(abstractor_abstraction, abstractor_abstraction_source, predicate_variant.downcase, sentence[:sentence], source[:source_id], source[:source_type].to_s, source[:source_method], source[:section_name],  nil, true, nil, nil, nil)
              end
            end
          end
        end
      end
    end
  end
end

#groupable? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 386

def groupable?
  !abstractor_subject_group_member.nil?
end

#suggest(abstractor_abstraction, abstractor_abstraction_source, match_value, sentence_match_value, source_id, source_type, source_method, section_name, suggested_value, unknown, not_applicable, custom_method, custom_explanation) ⇒ Object 



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# File 'lib/abstractor/methods/models/abstractor_subject.rb', line 306

def suggest(abstractor_abstraction, abstractor_abstraction_source, match_value, sentence_match_value, source_id, source_type, source_method, section_name, suggested_value, unknown, not_applicable, custom_method, custom_explanation)
  match_value.strip! unless match_value.nil?
  sentence_match_value.strip! unless sentence_match_value.nil?
  if abstractor_object_value?(suggested_value)
    abstractor_object_value = suggested_value
    suggested_value = suggested_value.value
  end
  abstractor_suggestion = abstractor_abstraction.detect_abstractor_suggestion(suggested_value, unknown, not_applicable)
  if !abstractor_suggestion
    abstractor_suggestion_status_needs_review = Abstractor::AbstractorSuggestionStatus.where(name: 'Needs review').first
    abstractor_suggestion = Abstractor::AbstractorSuggestion.create(
                                                        abstractor_abstraction: abstractor_abstraction,
                                                        abstractor_suggestion_status: abstractor_suggestion_status_needs_review,
                                                        suggested_value: suggested_value,
                                                        unknown: unknown,
                                                        not_applicable: not_applicable
                                                        )

    abstractor_suggestion.abstractor_suggestion_object_value = Abstractor::AbstractorSuggestionObjectValue.new(abstractor_object_value: abstractor_object_value) if abstractor_object_value
  end

  abstractor_suggestion_source = abstractor_suggestion.detect_abstractor_suggestion_source(abstractor_abstraction_source, sentence_match_value, source_id, source_type, source_method, section_name)
  if !abstractor_suggestion_source
    Abstractor::AbstractorSuggestionSource.create(
                                      abstractor_abstraction_source: abstractor_abstraction_source,
                                      abstractor_suggestion: abstractor_suggestion,
                                      match_value: match_value,
                                      sentence_match_value: sentence_match_value,
                                      source_id: source_id,
                                      source_type: source_type,
                                      source_method: source_method,
                                      section_name: section_name,
                                      custom_method: custom_method,
                                      custom_explanation: custom_explanation
                                     )
  end
  abstractor_suggestion
end