Class: Inferno::DSL::ValueExtractor

Inherits:
Object
  • Object
show all
Defined in:
lib/inferno/dsl/value_extractor.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(ig_resources, resource, profile_elements) ⇒ ValueExtractor

Returns a new instance of ValueExtractor.



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# File 'lib/inferno/dsl/value_extractor.rb', line 6

def initialize(ig_resources, resource, profile_elements)
  self.ig_resources = ig_resources
  self.resource = resource
  self.profile_elements = profile_elements
end

Instance Attribute Details

#ig_resources ⇒ Object

Returns the value of attribute ig_resources.



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# File 'lib/inferno/dsl/value_extractor.rb', line 4

def ig_resources
  @ig_resources
end

#profile_elements ⇒ Object

Returns the value of attribute profile_elements.



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# File 'lib/inferno/dsl/value_extractor.rb', line 4

def profile_elements
  @profile_elements
end

#resource ⇒ Object

Returns the value of attribute resource.



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# File 'lib/inferno/dsl/value_extractor.rb', line 4

def resource
  @resource
end

Instance Method Details

#bound_systems(the_element) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 50

def bound_systems(the_element)
  bound_systems_from_valueset(value_set(the_element))
end

#bound_systems_from_valueset(value_set) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 54

def bound_systems_from_valueset(value_set)
  value_set&.compose&.include&.map do |include_element|
    bound_systems_from_valueset_include_element(include_element)
  end&.flatten&.compact
end

#bound_systems_from_valueset_include_element(include_element) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 60

def bound_systems_from_valueset_include_element(include_element)
  if include_element.concept.present?
    include_element
  elsif whole_code_system_include?(include_element)
    whole_code_system(include_element)
  elsif include_element.valueSet.present?
    include_element.valueSet.map do |vs|
      a_value_set = ig_resources.value_set_by_url(vs)
      bound_systems_from_valueset(a_value_set)
    end
  end
end

#codes_from_system_code_pair(codings) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 89

def codes_from_system_code_pair(codings)
  codings.present? ? codings.map { |coding| coding[:code] }.compact.uniq : []
end

#codes_from_value_set_binding(the_element) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 85

def codes_from_value_set_binding(the_element)
  codes_from_system_code_pair(codings_from_value_set_binding(the_element))
end

#codings_from_bound_systems(bound_systems) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 107

def codings_from_bound_systems(bound_systems)
  return [] unless bound_systems.present?

  bound_systems.flat_map do |bound_system|
    case bound_system
    when FHIR::ValueSet::Compose::Include
      codings_from_include(bound_system)
    when FHIR::CodeSystem
      bound_system.concept.map { |concept| { system: bound_system.url, code: concept.code } }
    else
      []
    end
  end.uniq
end

#codings_from_include(include_element) ⇒ Object

A whole code system include becomes a system-only value



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# File 'lib/inferno/dsl/value_extractor.rb', line 123

def codings_from_include(include_element)
  return [{ system: include_element.system }] if include_element.concept.blank?

  include_element.concept.map { |concept| { system: include_element.system, code: concept.code } }
end

#codings_from_value_set_binding(the_element) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 93

def codings_from_value_set_binding(the_element)
  return [] if the_element.nil?

  bound_systems = bound_systems(the_element)

  return codings_from_bound_systems(bound_systems) if bound_systems.present?

  expansion_contains = value_set_expansion_contains(the_element)

  return [] if expansion_contains.blank?

  expansion_contains.map { |contains| { system: contains.system, code: contains.code } }.compact.uniq
end

#fhir_metadata(current_path) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 133

def fhir_metadata(current_path)
  FHIR.const_get(resource)::METADATA[current_path]
end

#value_set(the_element) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 46

def value_set(the_element)
  ig_resources.value_set_by_url(value_set_binding(the_element)&.valueSet)
end

#value_set_binding(the_element) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 42

def value_set_binding(the_element)
  the_element&.binding
end

#value_set_expansion_contains(element) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 129

def value_set_expansion_contains(element)
  value_set(element)&.expansion&.contains
end

#values_from_fixed_codes(profile_element, type) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 12

def values_from_fixed_codes(profile_element, type)
  return [] unless type == 'CodeableConcept'

  elements = profile_elements.select do |element|
    element.path == "#{profile_element.path}.coding.code" && element.fixedCode.present?
  end

  elements.map(&:fixedCode)
end

#values_from_pattern_codeable_concept(profile_element, type) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 32

def values_from_pattern_codeable_concept(profile_element, type)
  return [] unless type == 'CodeableConcept'

  elements = profile_elements.select do |element|
    element.path == profile_element.path && element.patternCodeableConcept.present? && element.min.positive?
  end

  elements.map { |element| element.patternCodeableConcept.coding.first.code }
end

#values_from_pattern_coding(profile_element, type) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 22

def values_from_pattern_coding(profile_element, type)
  return [] unless type == 'CodeableConcept'

  elements = profile_elements.select do |element|
    element.path == "#{profile_element.path}.coding" && element.patternCoding.present?
  end

  elements.map { |element| element.patternCoding.code }
end

#values_from_resource_metadata(paths) ⇒ Object 



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# File 'lib/inferno/dsl/value_extractor.rb', line 137

def values_from_resource_metadata(paths)
  values = []

  paths.each do |current_path|
    current_metadata = fhir_metadata(current_path)

    next unless current_metadata&.dig('valid_codes').present?

    values += current_metadata['valid_codes'].flat_map do |system, codes|
      codes.map { |code| { system:, code: } }
    end
  end

  values
end

#whole_code_system(include_element) ⇒ Object

An include of a whole code system lists no codes. Use the code system's concepts when the IG has them, otherwise keep the include so that any code from its system is accepted.



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# File 'lib/inferno/dsl/value_extractor.rb', line 80

def whole_code_system(include_element)
  code_system = ig_resources.code_system_by_url(include_element.system)
  code_system&.concept.present? ? code_system : include_element
end

#whole_code_system_include?(include_element) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/inferno/dsl/value_extractor.rb', line 73

def whole_code_system_include?(include_element)
  include_element.system.present? && include_element.concept.blank? &&
    include_element.filter&.empty? && include_element.valueSet.blank?
end