Module: CancerRegistryReportingTestKit::HDEABundleParse

Extended by:
Forwardable
Includes:
FHIRResourceNavigation
Included in:
CancerRegistryReportingTestKit::HDEAV100::CcrrContentBundleParseAndValidationTest, MustSupportTest
Defined in:
lib/cancer_registry_reporting_test_kit/bundle_parse.rb

Constant Summary collapse

CODE_TO_URL_MAP = 
{
  '363346000' => 'http://hl7.org/fhir/us/central-cancer-registry-reporting/StructureDefinition/central-cancer-registry-primary-cancer-condition',
  '128462008' => 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-secondary-cancer-condition',
  '21908-9' => 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-stage-group',
  '1217123003' => 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-radiotherapy-course-summary',
  '11450-4' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition',
  '48765-2' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance',
  '74165-2' => 'http://hl7.org/fhir/us/odh/StructureDefinition/odh-UsualWork',
  '47519-4' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure',
  '8716-3' => 'http://hl7.org/fhir/StructureDefinition/Observation',
  '29762-2' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus'
}.freeze
CODE_TO_MULTIPLE_ENTRY_RESOURCE_MAP = 
{
  '29549-3' => {
    'MedicationAdministration' => 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-related-medication-administration', 'Medication' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication'
  },
  '10160-0' => {
    'MedicationAdministration' => 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-related-medication-administration', 'MedicationStatement' => 'http://hl7.org/fhir/StructureDefinition/MedicationStatement', 'Medication' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication'
  },
  '30954-2' => { 'Observation' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab',
                 'DiagnosticReport' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-lab' },
  '28650-0' => { 'DocumentReference' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference',
                 'DiagnosticReport' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note' },
  '18776-5' => {
    'MedicationRequest' => 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-related-medication-request', 'Medication' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication', 'ServiceRequest' => 'http://hl7.org/fhir/StructureDefinition/ServiceRequest', 'CarePlan' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan'
  }
}.freeze
FIELD_TO_URL_MAP = 
{
  'subject' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient',
  'encounter' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter',
  'author' => ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole',
               'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner', 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization']
}.freeze

Constants included from FHIRResourceNavigation

FHIRResourceNavigation::DAR_EXTENSION_URL, FHIRResourceNavigation::PRIMITIVE_DATA_TYPES

Instance Method Summary collapse

Methods included from FHIRResourceNavigation

#find_a_value_at, #find_slice_via_discriminator, #get_next_value, #get_primitive_type_value, #resolve_path, #verify_slice_by_values

Instance Method Details

#clear_unresolved_references ⇒ Object 



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# File 'lib/cancer_registry_reporting_test_kit/bundle_parse.rb', line 22

def clear_unresolved_references
  @unresolved_references = []
end

#find_resource_in_bundle(reference, bundle) ⇒ Object

TODO: we may have to be more comprehensive with checks for references - TBD



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# File 'lib/cancer_registry_reporting_test_kit/bundle_parse.rb', line 155

def find_resource_in_bundle(reference, bundle)
  bundle.entry.find do |res|
    res.resource.id == reference.split('/').last && res.resource.resourceType == reference.split('/').first
  end&.resource
end

#look_for_references_in_resource(resource, bundle) ⇒ Object

Helpers



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# File 'lib/cancer_registry_reporting_test_kit/bundle_parse.rb', line 85

def look_for_references_in_resource(resource, bundle)
  resource_hash = {}
  resource.to_hash.each_key do |key|
    value = resource&.send(key.to_sym)
    if value.is_a?(FHIR::Reference)
      resource_hash[FIELD_TO_URL_MAP[key]] ||= []
      referenced_resource = find_resource_in_bundle(value.reference, bundle)
      unresolved_references << value.reference unless referenced_resource
      if !resource_hash[FIELD_TO_URL_MAP[key]].include?(referenced_resource) && referenced_resource
        resource_hash[FIELD_TO_URL_MAP[key]] << referenced_resource
      end
    elsif value.is_a?(Array) && value.all? { |elmt| elmt.is_a?(FHIR::Composition::Section) }
      resource_hash.merge!(parse_sections(value, bundle))
    elsif value.is_a?(Array) && value.all? { |elmt| elmt.is_a?(FHIR::Reference) }
      resource_hash[FIELD_TO_URL_MAP[key]] ||= []
      value.each do |val|
        referenced_resource = find_resource_in_bundle(val.reference, bundle)
        unresolved_references << val.reference unless referenced_resource
        if !resource_hash[FIELD_TO_URL_MAP[key]].include?(referenced_resource) && referenced_resource
          resource_hash[FIELD_TO_URL_MAP[key]] << referenced_resource
        end
      end
    elsif value.is_a?(FHIR::Model)
      resource_hash.merge!(look_for_references_in_resource(value, bundle))
    elsif value.is_a?(Array) && value.all? { |elmt| elmt.is_a?(FHIR::Model) }
      value.each { |val| resource_hash.merge!(look_for_references_in_resource(val, bundle)) }
    end
  end
  resource_hash.reject { |_k, v| v.nil? || v&.empty? }
end

#multiple_reference_types?(code) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/cancer_registry_reporting_test_kit/bundle_parse.rb', line 146

def multiple_reference_types?(code)
  CODE_TO_MULTIPLE_ENTRY_RESOURCE_MAP.keys.include?(code)
end

#parse_bundle(bundle, index) ⇒ Object

Method for translating received bundle into a hash of resources. Use for MS and Validation testing



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# File 'lib/cancer_registry_reporting_test_kit/bundle_parse.rb', line 63

def parse_bundle(bundle, index)
  first_resource = bundle.entry.first.resource
  if first_resource.is_a?(FHIR::Composition)
    parsed_bundle = look_for_references_in_resource(first_resource, bundle)
    parsed_bundle['http://hl7.org/fhir/us/central-cancer-registry-reporting/StructureDefinition/ccrr-content-bundle'] ||= []
    parsed_bundle['http://hl7.org/fhir/us/central-cancer-registry-reporting/StructureDefinition/ccrr-content-bundle'].push(bundle)
    parsed_bundle['http://hl7.org/fhir/us/central-cancer-registry-reporting/StructureDefinition/ccrr-composition'] ||= []
    parsed_bundle['http://hl7.org/fhir/us/central-cancer-registry-reporting/StructureDefinition/ccrr-composition'].push(first_resource)
    unless unresolved_references.empty?
      warning "The following references did not resolve, the resources either do not exist in the bundle or are mislabeled: #{unresolved_references}"
    end
    current_bundle_unresolved_references = unresolved_references
    clear_unresolved_references
    [parsed_bundle, current_bundle_unresolved_references]
  else
    add_message('error', "Unable to parse bundle #{index + 1}: " \
                         "the first entry must be a Composition but got #{first_resource.resourceType}.")
    [nil, nil]
  end
end

#parse_sections(sections, bundle) ⇒ Object 



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# File 'lib/cancer_registry_reporting_test_kit/bundle_parse.rb', line 116

def parse_sections(sections, bundle)
  sections.each_with_object({}) do |sec, hash|
    code = sec.code.coding.first.code
    if multiple_reference_types?(code)
      sec.entry.each do |ref|
        referenced_resource = find_resource_in_bundle(ref.reference, bundle)
        if referenced_resource
          hash[profile_from_resource_type(code, referenced_resource.resourceType)] ||= []
          unless hash[profile_from_resource_type(code,
                                                 referenced_resource.resourceType)].include?(referenced_resource)
            hash[profile_from_resource_type(code, referenced_resource.resourceType)] << referenced_resource
          end
        else
          unresolved_references << ref.reference
        end
      end
    else
      resource_key = CODE_TO_URL_MAP[code]
      hash[resource_key] ||= []
      sec.entry.each do |ref|
        referenced_resource = find_resource_in_bundle(ref.reference, bundle)
        unresolved_references << ref.reference unless referenced_resource
        if !hash[resource_key].include?(referenced_resource) && referenced_resource
          hash[resource_key] << referenced_resource
        end
      end
    end
  end
end

#profile_from_resource_type(code, resource_type) ⇒ Object 



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# File 'lib/cancer_registry_reporting_test_kit/bundle_parse.rb', line 150

def profile_from_resource_type(code, resource_type)
  CODE_TO_MULTIPLE_ENTRY_RESOURCE_MAP[code][resource_type]
end

#unresolved_references ⇒ Object

Much of this is extremely custom fit to HDEA. HDEA Custom Components:

  • CODE_TO_URL_MAP, CODE_TO_MULTIPLE_ENTRY_RESOURCE_MAP, FIELD_TO_URL_MAP are nongenerated mappings specific to HDEA.

  • The ‘profile_from_resource_type()` method similarly assumes decisions between profiles are made via code. This is NOT what the IG suggests (instead verify by profile)

  • The ‘parse_bundle()` method assumes the bundle is a content bundle for hdea and thus starts with a composition resource. It also immediately yields unresolved references as an info message

  • The ‘look_for_references_in_resource()` method was designed to be flexible but with HDEA CCRR as the grounds for inspiration. It has not been tested on other bundles that include a composition.

  • Assumes references are of the form ‘ResourceType/ID`



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# File 'lib/cancer_registry_reporting_test_kit/bundle_parse.rb', line 18

def unresolved_references
  @unresolved_references ||= []
end