Class: Inferno::DSL::MustSupportMetadataExtractor

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

Overview

The MustSupportMetadataExtractor takes a StructureDefinition and parses it into a hash-based metadata that simplifies checking for MustSupport elements. MustSupport elements may be either plain elements, extensions, or slices. This logic was originally developed for the US Core Test Kit and has been migrated into Inferno core.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(profile_elements, profile, resource, ig_resources, requirement_extension_url = nil) ⇒ MustSupportMetadataExtractor

Construct a new extractor

Parameters:

  • profile_elements (Array<FHIR::ElementDefinition>) —

    the elements of the profile to consider, ie, profile.snapshot.element

  • profile (FHIR::StructureDefinition) —

    the profile to parse

  • resource (String) —

    the resourceType that the profile applies to, ie, profile.type

  • ig_resources (Inferno::Entities::IG)
  • requirement_extension_url (String) (defaults to: nil) —

    the URL of an extension to flag elements as required even if not MS



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 19

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

Instance Attribute Details

#ig_resources ⇒ Object

Returns the value of attribute ig_resources.



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 10

def ig_resources
  @ig_resources
end

#profile ⇒ Object

Returns the value of attribute profile.



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 10

def profile
  @profile
end

#profile_elements ⇒ Object

Returns the value of attribute profile_elements.



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 10

def profile_elements
  @profile_elements
end

#requirement_extension_url ⇒ Object

Returns the value of attribute requirement_extension_url.



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 10

def requirement_extension_url
  @requirement_extension_url
end

#resource ⇒ Object

Returns the value of attribute resource.



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 10

def resource
  @resource
end

Instance Method Details

#all_must_support_elements ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 44

def all_must_support_elements
  profile_elements.select { |element| element.mustSupport || by_requirement_extension_only?(element) }
end

#by_requirement_extension_only?(element) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 37

def by_requirement_extension_only?(element)
  requirement_extension_url && !element.mustSupport &&
    element.extension.any? do |extension|
      extension.url == requirement_extension_url && extension.valueBoolean
    end
end

#discriminator_path(discriminator) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 142

def discriminator_path(discriminator)
  if discriminator.path == '$this'
    ''
  elsif discriminator.path.start_with?('$this.')
    discriminator.path[6..]
  else
    discriminator.path
  end
end

#discriminators(slice) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 76

def discriminators(slice)
  slice&.slicing&.discriminator
end

#element_part_of_slice_discrimination?(element) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 239

def element_part_of_slice_discrimination?(element)
  must_support_slice_elements.any? { |ms_slice| element.id.include?(ms_slice.id) }
end

#extract_required_binding_values(pattern_element, metadata) ⇒ Object 



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

def extract_required_binding_values(pattern_element, metadata)
  value_extractor = ValueExtractor.new(ig_resources, resource, profile_elements)

  value_extractor.codings_from_value_set_binding(pattern_element).presence ||
    value_extractor.values_from_resource_metadata([metadata[:path]]).presence || []
end

#extract_supported_types(current_element) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 355

def extract_supported_types(current_element)
  current_element.type.select { |type| save_type_code?(type) }.map(&:code)
end

#extract_target_profiles(type) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 292

def extract_target_profiles(type)
  target_profiles = []

  if type.targetProfile&.length == 1
    target_profiles << type.targetProfile.first
  else
    type.source_hash['_targetProfile']&.each_with_index do |hash, index|
      if hash.present?
        element = FHIR::Element.new(hash)
        target_profiles << type.targetProfile[index] if type_must_support_extension?(element.extension)
      end
    end
  end

  target_profiles
end

#find_element_by_discriminator_path(current_element, discriminator_path) ⇒ Object 



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

def find_element_by_discriminator_path(current_element, discriminator_path)
  if discriminator_path.present?
    profile_elements.find { |element| element.id == "#{current_element.id}.#{discriminator_path}" } ||
      profile_elements.find { |element| element.id == "#{current_element.path}.#{discriminator_path}" }
  else
    current_element
  end
end

#get_type_must_support_metadata(current_metadata, current_element) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 268

def get_type_must_support_metadata(current_metadata, current_element)
  current_element.type.map do |type|
    next unless type_must_support_extension?(type.extension)

    metadata =
      {
        path: "#{current_metadata[:path].delete_suffix('[x]')}#{type.code.upcase_first}",
        original_path: current_metadata[:path]
      }
    metadata[:types] = [type.code] if save_type_code?(type)
    handle_type_must_support_target_profiles(type, metadata) if type.code == 'Reference'

    metadata
  end.compact
end

#handle_choice_type_in_sliced_element(current_metadata, must_support_elements_metadata) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 309

def handle_choice_type_in_sliced_element(current_metadata, must_support_elements_metadata)
  choice_element_metadata = must_support_elements_metadata.find do |metadata|
    metadata[:original_path].present? &&
      current_metadata[:path].include?(metadata[:original_path])
  end

  return unless choice_element_metadata.present?

  current_metadata[:original_path] = current_metadata[:path]
  current_metadata[:path] =
    current_metadata[:path].sub(choice_element_metadata[:original_path], choice_element_metadata[:path])
end

#handle_fixed_values(metadata, element) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 243

def handle_fixed_values(metadata, element)
  if element.fixed.present?
    metadata[:fixed_value] = element.fixed
  elsif element.patternCodeableConcept.present? && !element_part_of_slice_discrimination?(element)
    metadata[:fixed_value] = element.patternCodeableConcept.coding.first.code
    metadata[:path] += '.coding.code'
  elsif element.fixedCode.present?
    metadata[:fixed_value] = element.fixedCode
  elsif element.patternIdentifier.present? && !element_part_of_slice_discrimination?(element)
    metadata[:fixed_value] = element.patternIdentifier.system
    metadata[:path] += '.system'
  end
end

#handle_type_must_support_target_profiles(type, metadata) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 284

def handle_type_must_support_target_profiles(type, metadata)
  target_profiles = extract_target_profiles(type)

  # remove target_profile for FHIR Base resource type.
  target_profiles.delete_if { |reference| reference.start_with?('http://hl7.org/fhir/StructureDefinition') }
  metadata[:target_profiles] = target_profiles if target_profiles.present?
end

#must_support_elements ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 322

def must_support_elements
  must_support_elements_metadata = []
  plain_must_support_elements.each do |current_element|
    current_metadata = {
      path: current_element.id.gsub("#{resource}.", '')
    }
    current_metadata[:by_requirement_extension_only] = true if by_requirement_extension_only?(current_element)

    type_must_support_metadata = get_type_must_support_metadata(current_metadata, current_element)

    if type_must_support_metadata.any?
      must_support_elements_metadata.concat(type_must_support_metadata)
    else
      handle_choice_type_in_sliced_element(current_metadata, must_support_elements_metadata)

      supported_types = extract_supported_types(current_element)
      current_metadata[:types] = supported_types if supported_types.present?

      if current_element.type.first&.code == 'Reference'
        handle_type_must_support_target_profiles(current_element.type.first,
                                                 current_metadata)
      end

      handle_fixed_values(current_metadata, current_element)

      remove_conflicting_metadata_without_fixed_value(must_support_elements_metadata, current_metadata)

      must_support_elements_metadata << current_metadata
    end
  end
  must_support_elements_metadata.uniq
end

#must_support_extension_elements ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 48

def must_support_extension_elements
  all_must_support_elements.select { |element| element.path.end_with? 'extension' }
end

#must_support_extensions ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 52

def must_support_extensions
  must_support_extension_elements.map do |element|
    {
      id: element.id,
      path: element.path.gsub("#{resource}.", ''),
      url: element.type.first.profile.first
    }.tap do |metadata|
      metadata[:by_requirement_extension_only] = true if by_requirement_extension_only?(element)
    end
  end
end

#must_support_slice_elements ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 64

def must_support_slice_elements
  all_must_support_elements.select do |element|
    !element.path.end_with?('extension') && element.sliceName.present?
  end
end

#must_support_slices ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 231

def must_support_slices
  type_slices + value_slices
end

#must_support_type_slice_elements ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 136

def must_support_type_slice_elements
  must_support_slice_elements.select do |element|
    discriminators(sliced_element(element))&.first&.type == 'type'
  end
end

#must_support_value_slice_elements ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 174

def must_support_value_slice_elements
  must_support_slice_elements.select do |element|
    # discriminator type 'pattern' is deprecated in FHIR R5 and made equivalent to 'value'
    ['value', 'pattern'].include?(discriminators(sliced_element(element))&.first&.type)
  end
end

#must_supports ⇒ Hash

Retrieval method for the must support metadata

Returns:

  • (Hash) 


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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 29

def must_supports
  @must_supports ||= {
    extensions: must_support_extensions,
    slices: must_support_slices,
    elements: must_support_elements
  }
end

#plain_must_support_elements ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 235

def plain_must_support_elements
  all_must_support_elements - must_support_extension_elements - must_support_slice_elements
end

#remove_conflicting_metadata_without_fixed_value(must_support_elements_metadata, current_metadata) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 359

def remove_conflicting_metadata_without_fixed_value(must_support_elements_metadata, current_metadata)
  must_support_elements_metadata.delete_if do |metadata|
    metadata[:path] == current_metadata[:path] && metadata[:fixed_value].blank?
  end
end

#required_binding_pattern?(pattern_element) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 125

def required_binding_pattern?(pattern_element)
  pattern_element.binding&.strength == 'required' && pattern_element.binding&.valueSet
end

#save_pattern_slice(pattern_element, discriminator_path, metadata) ⇒ Object 



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

def save_pattern_slice(pattern_element, discriminator_path, metadata)
  if pattern_element.patternCodeableConcept
    {
      type: 'patternCodeableConcept',
      path: discriminator_path,
      code: pattern_element.patternCodeableConcept.coding.first.code,
      system: pattern_element.patternCodeableConcept.coding.first.system
    }
  elsif pattern_element.patternCoding
    {
      type: 'patternCoding',
      path: discriminator_path,
      code: pattern_element.patternCoding.code,
      system: pattern_element.patternCoding.system
    }
  elsif pattern_element.patternIdentifier
    {
      type: 'patternIdentifier',
      path: discriminator_path,
      system: pattern_element.patternIdentifier.system
    }
  elsif required_binding_pattern?(pattern_element)
    {
      type: 'requiredBinding',
      path: discriminator_path,
      values: extract_required_binding_values(pattern_element, metadata)
    }
  else
    # prevent errors in case an IG does something different
    {
      type: 'unsupported',
      path: discriminator_path
    }
  end
end

#save_type_code?(type) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 264

def save_type_code?(type)
  type.code == 'Reference'
end

#sliced_element(slice) ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 70

def sliced_element(slice)
  profile_elements.find do |element|
    element.id == slice.path || element.id == slice.id.sub(":#{slice.sliceName}", '')
  end
end

#type_must_support_extension?(extensions) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 257

def type_must_support_extension?(extensions)
  extensions&.any? do |extension|
    extension.url == 'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support' &&
      extension.valueBoolean
  end
end

#type_slices ⇒ Object 



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 152

def type_slices
  must_support_type_slice_elements.map do |current_element|
    discriminator = discriminators(sliced_element(current_element)).first
    type_path = discriminator_path(discriminator)
    type_element = find_element_by_discriminator_path(current_element, type_path)

    type_code = type_element.type.first.code

    {
      slice_id: current_element.id,
      slice_name: current_element.sliceName,
      path: current_element.path.gsub("#{resource}.", ''),
      discriminator: {
        type: 'type',
        code: type_code.upcase_first
      }
    }.tap do |metadata|
      metadata[:by_requirement_extension_only] = true if by_requirement_extension_only?(current_element)
    end
  end
end

#value_slices ⇒ Object

rubocop:disable Metrics/CyclomaticComplexity



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# File 'lib/inferno/dsl/must_support_metadata_extractor.rb', line 181

def value_slices # rubocop:disable Metrics/CyclomaticComplexity
  must_support_value_slice_elements.map do |current_element|
    {
      slice_id: current_element.id,
      slice_name: current_element.sliceName,
      path: current_element.path.gsub("#{resource}.", '')
    }.tap do |metadata|
      fixed_values = []
      pattern_value = {}

      element_discriminators = discriminators(sliced_element(current_element))

      element_discriminators.each do |discriminator|
        discriminator_path = discriminator_path(discriminator)
        pattern_element = find_element_by_discriminator_path(current_element, discriminator_path)

        # This is a workaround for a known version of a profile that has a bad discriminator:
        # the discriminator refers to a nested field within a CodeableConcept,
        # but the profile doesn't contain an element definition for it, so there's no way to
        # define a fixed value on the element to define the slice.
        # In this instance the element has a second (good) discriminator on the CodeableConcept field itself,
        # and in subsequent versions of the profile, the bad discriminator was removed.
        next if pattern_element.nil? && element_discriminators.length > 1

        if pattern_element.fixed.present?
          fixed_values << {
            path: discriminator_path,
            value: pattern_element.fixed
          }
        elsif pattern_value.present?
          raise StandardError, "Found more than one pattern slices for the same element #{pattern_element}."
        else
          pattern_value = save_pattern_slice(pattern_element, discriminator_path, metadata)
        end
      end

      if fixed_values.present?
        metadata[:discriminator] = {
          type: 'value',
          values: fixed_values
        }
      elsif pattern_value.present?
        metadata[:discriminator] = pattern_value
      end

      metadata[:by_requirement_extension_only] = true if by_requirement_extension_only?(current_element)
    end
  end
end