Class: USCoreTestKit::Generator::MustSupportMetadataExtractor

Inherits:
Object
  • Object
show all
Defined in:
lib/us_core_test_kit/generator/must_support_metadata_extractor.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(profile_elements, profile, resource, ig_resources) ⇒ MustSupportMetadataExtractor

Returns a new instance of MustSupportMetadataExtractor.



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 13

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

Instance Attribute Details

#ig_resources ⇒ Object

Returns the value of attribute ig_resources.



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 11

def ig_resources
  @ig_resources
end

#profile ⇒ Object

Returns the value of attribute profile.



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 11

def profile
  @profile
end

#profile_elements ⇒ Object

Returns the value of attribute profile_elements.



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 11

def profile_elements
  @profile_elements
end

#resource ⇒ Object

Returns the value of attribute resource.



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 11

def resource
  @resource
end

Instance Method Details

#all_must_support_elements ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 39

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

#discriminators(slice) ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 69

def discriminators(slice)
  slice.slicing.discriminator
end

#element_part_of_slice_discrimination?(element) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 219

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

#get_type_must_support_metadata(current_metadata, current_element) ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 249

def get_type_must_support_metadata(current_metadata, current_element)
  current_element.type.map do |type|
    if 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
  end.compact
end

#handle_choice_type_in_sliced_element(current_metadata, must_support_elements_metadata) ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 288

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

  if 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
end

#handle_fixed_values(metadata, element) ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 224

def handle_fixed_values(metadata, element)
  if element.fixedUri.present?
    metadata[:fixed_value] = element.fixedUri
  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_special_cases ⇒ Object

SPECIAL CASE ####



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 335

def handle_special_cases
  remove_vital_sign_component
  remove_blood_pressure_value_data_absent_reason
  remove_observation_data_absent_reason

  case profile.version
  when '3.1.1'
    MustSupportMetadataExtractorUsCore3.new(profile, @must_supports).handle_special_cases
  when '4.0.0'
    MustSupportMetadataExtractorUsCore4.new(profile, @must_supports).handle_special_cases
  when '5.0.1'
    MustSupportMetadataExtractorUsCore5.new(profile, @must_supports).handle_special_cases
  when '6.1.0'
    MustSupportMetadataExtractorUsCore6.new(profile, @must_supports).handle_special_cases
  when '7.0.0'
    MustSupportMetadataExtractorUsCore7.new(profile, @must_supports).handle_special_cases
  end
end

#handle_type_must_support_target_profiles(type, metadata) ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 265

def handle_type_must_support_target_profiles(type, metadata)
  # US Core 3.1.1 profiles do not have US Core target profiles.
  # Vital Sign proifles from FHIR R4 (version 4.0.1) do not have US Core target profiles either.
  return if ['3.1.1', '4.0.1'].include?(profile.version)

  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

  # 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

#is_blood_pressure? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 361

def is_blood_pressure?
  ['bp', 'us-core-blood-pressure', 'us-core-average-blood-pressure'].include?(profile.id)
end

#is_uscdi_requirement_element?(element) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 32

def is_uscdi_requirement_element?(element)
  element.extension.any? do |extension|
    extension.url == 'http://hl7.org/fhir/us/core/StructureDefinition/uscdi-requirement' &&
    extension.valueBoolean
  end && !element.mustSupport
end

#is_vital_sign? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 354

def is_vital_sign?
  [
    'http://hl7.org/fhir/StructureDefinition/vitalsigns',
    'http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs'
  ].include?(profile.baseDefinition)
end

#must_support_elements ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 300

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

      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 = current_element.type.select { |type| save_type_code?(type) }.map { |type| type.code }
        current_metadata[:types] = supported_types if supported_types.present?

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

        handle_fixed_values(current_metadata, current_element)

        must_support_elements_metadata.delete_if do |metadata|
          metadata[:path] == current_metadata[:path] && metadata[:fixed_value].blank?
        end

        must_support_elements_metadata << current_metadata
      end
    end
  end.uniq
end

#must_support_extension_elements ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 43

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/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 47

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|
      if is_uscdi_requirement_element?(element)
        metadata[:uscdi_only] = true
      end
    end
  end
end

#must_support_pattern_slice_elements ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 73

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

#must_support_slice_elements ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 61

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

#must_support_slices ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 211

def must_support_slices
  pattern_slices + type_slices + value_slices
end

#must_support_type_slice_elements ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 140

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/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 176

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

#must_supports ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 20

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

  handle_special_cases

  @must_supports
end

#pattern_slices ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 79

def pattern_slices
  must_support_pattern_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|
      discriminator = discriminators(sliced_element(current_element)).first
      discriminator_path = discriminator.path
      discriminator_path = '' if discriminator_path == '$this'
      pattern_element =
        if discriminator_path.present?
          profile_elements.find { |element| element.id == "#{current_element.id}.#{discriminator_path}" }
        else
          current_element
        end
      metadata[:discriminator] =
        if pattern_element.patternCodeableConcept.present?
          {
            type: 'patternCodeableConcept',
            path: discriminator_path,
            code: pattern_element.patternCodeableConcept.coding.first.code,
            system: pattern_element.patternCodeableConcept.coding.first.system
          }
        elsif pattern_element.patternCoding.present?
          {
            type: 'patternCoding',
            path: discriminator_path,
            code: pattern_element.patternCoding.code,
            system: pattern_element.patternCoding.system
          }
        elsif pattern_element.patternIdentifier.present?
          {
            type: 'patternIdentifier',
            path: discriminator_path,
            system: pattern_element.patternIdentifier.system
          }
        elsif pattern_element.binding&.strength == 'required' &&
              pattern_element.binding&.valueSet.present?

          value_extractor = ValueExactor.new(ig_resources, resource, profile_elements)

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

          {
            type: 'requiredBinding',
            path: discriminator_path,
            values: values
          }
        else
          raise StandardError, 'Unsupported discriminator pattern type'
        end

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

#plain_must_support_elements ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 215

def plain_must_support_elements
  plain_must_supports = all_must_support_elements - must_support_extension_elements - must_support_slice_elements
end

#remove_blood_pressure_value_data_absent_reason ⇒ Object

Exclude Observation.value[x] from observation-bp



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 377

def remove_blood_pressure_value_data_absent_reason
  return unless is_blood_pressure?

  pattern = /component(:[^.]+)?\.dataAbsentReason/

  @must_supports[:elements].delete_if do |element|
    element[:path].start_with?('value[x]') ||
    element[:original_path]&.start_with?('value[x]') ||
    element[:path] == ('dataAbsentReason') ||
    (
      pattern.match?(element[:path]) && ['3.1.1', '4.0.0'].include?(ig_resources.ig.version)
    )
  end

  @must_supports[:slices].delete_if do |slice|
    slice[:path].start_with?('value[x]')
  end
end

#remove_observation_data_absent_reason ⇒ Object

ONC and US Core 4.0.0 both clarified that health IT developers that always provide HL7 FHIR “observation” values are not required to demonstrate Health IT Module support for “dataAbsentReason” elements. Remove MS check for dataAbsentReason and component.dataAbsentReason from vital sign profiles and observation lab profile Smoking status profile does not have MS on dataAbsentReason. It is safe to use profile.type == ‘Observation’ Since US Core 5.0.1, Blood Pressure profile restores component.dataAbsentReason as MustSupport.



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 401

def remove_observation_data_absent_reason
  return if is_blood_pressure?

  pattern = /(component(:[^.]+)?\.)?dataAbsentReason/

  if profile.type == 'Observation'
    @must_supports[:elements].delete_if do |element|
      pattern.match?(element[:path])
    end
  end
end

#remove_vital_sign_component ⇒ Object

Exclude Observation.component from vital sign profiles except observation-bp and observation-pulse-ox



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 366

def remove_vital_sign_component
  return if is_blood_pressure? || profile.name == 'USCorePulseOximetryProfile'

  if is_vital_sign?
    @must_supports[:elements].delete_if do |element|
      element[:path].start_with?('component')
    end
  end
end

#save_type_code?(type) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 245

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

#sliced_element(slice) ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 65

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

#type_must_support_extension?(extensions) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 238

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/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 146

def type_slices
  must_support_type_slice_elements.map do |current_element|
    discriminator = discriminators(sliced_element(current_element)).first
    type_path = discriminator.path
    type_path = '' if type_path == '$this'
    type_element =
      if type_path.present?
        elements.find { |element| element.id == "#{current_element.id}.#{type_path}" }
      else
        current_element
      end

    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|
      if is_uscdi_requirement_element?(current_element)
        metadata[:uscdi_only] = true
      end
    end
  end
end

#value_slices ⇒ Object 



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# File 'lib/us_core_test_kit/generator/must_support_metadata_extractor.rb', line 182

def value_slices
  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}.", ''),
      discriminator: {
        type: 'value'
      }
    }.tap do |metadata|
      metadata[:discriminator][:values] = discriminators(sliced_element(current_element)).map do |discriminator|
        fixed_element = profile_elements.find do |element|
          element.id.starts_with?(current_element.id) &&
            element.path == "#{current_element.path}.#{discriminator.path}"
        end

        {
          path: discriminator.path,
          value: fixed_element.fixedUri || fixed_element.fixedCode
        }
      end

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