Class: Inferno::DSL::FHIREvaluation::Rules::ValueSetsDemonstrate

Inherits:
Inferno::DSL::FHIREvaluation::Rule show all
Defined in:
lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb

Overview

Algorithm: 1. Extract pairs of system and code from include in value sets in IG 2. If valueSet exists in include, retrieve the value sets from UMLS. Extract pairs of system and code from the result. 3. For each pair of system and code, check if any resources in the IG have instance of them. 4. Count total number of existences.

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#config ⇒ Object

Returns the value of attribute config.


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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 25

def config
  @config
end

#value_set_unevaluated ⇒ Object

Returns the value of attribute value_set_unevaluated.


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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 25

def value_set_unevaluated
  @value_set_unevaluated
end

#value_set_unused ⇒ Object

Returns the value of attribute value_set_unused.


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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 25

def value_set_unused
  @value_set_unused
end

#value_set_used ⇒ Object

Returns the value of attribute value_set_used.


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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 25

def value_set_used
  @value_set_used
end

Instance Method Details

#check(context) ⇒ Object

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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 27

def check(context)
  @config = context.config
  @value_set_used = []
  @value_set_unused = []
  @value_set_unevaluated = []

  classify_valuesets(context)

  context.add_result create_result_message
end

#classify_valuesets(context) ⇒ Object

rubocop:disable Metrics/CyclomaticComplexity

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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 39

def classify_valuesets(context)
  context.ig.value_sets.each do |valueset|
    valueset_used_count = 0
    system_codes = extract_systems_codes_from_valueset(valueset)

    value_set_unevaluated << "#{valueset.url}: unable to find system and code" if system_codes.none?
    value_set_unevaluated.uniq!

    next if value_set_unevaluated.any? { |element| element.include?(valueset.url) }

    resource_used = []

    context.data.each do |resource|
      system_codes.each do |system_code|
        next unless !system_code.nil? && resource_uses_code(resource.to_hash, system_code[:system],
                                                            system_code[:code])

        valueset_used_count += 1
        resource_used << resource.id unless resource_used.include?(resource.id)
      end
    end

    if valueset_used_count.positive?
      # rubocop:disable Layout/LineLength
      value_set_used << "#{valueset.url} is used #{valueset_used_count} times in #{resource_used.count} resources"
      # rubocop:enable Layout/LineLength
    else
      value_set_unused << valueset.url
    end
  end
end

#create_result_message ⇒ Object

rubocop:disable Metrics/CyclomaticComplexity

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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 73

def create_result_message
  if value_set_unused.none?
    message = 'All ValueSets are used in examples:'
    value_set_used.map { |value_set| message += "\n\t#{value_set}" }

    if value_set_unevaluated.any?
      message += "\nThe following Value Sets were not able to be evaluated: "
      value_set_unevaluated.map { |value_set| message += "\n\t#{value_set}" }
    end

    EvaluationResult.new(message, severity: 'success', rule: self)
  else
    message = 'Found ValueSets with all codes used (at least once) in examples:'
    value_set_used.map { |url| message += "\n\t#{url}" }

    message += "\nFound unused ValueSets: "
    value_set_unused.map { |url| message += "\n\t#{url}" }

    if value_set_unevaluated.any?
      message += "\nFound unevaluated ValueSets: "
      value_set_unevaluated.map { |url| message += "\n\t#{url}" }
    end

    EvaluationResult.new(message, rule: self)
  end
end

#extract_systems_codes_from_valueset(valueset) ⇒ Object

rubocop:disable Metrics/CyclomaticComplexity

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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 102

def extract_systems_codes_from_valueset(valueset)
  system_codes = []

  if valueset.to_hash['compose']
    valueset.to_hash['compose']['include'].each do |include|
      if include['valueSet']
        include['valueSet'].each do |url|
          retrieve_valueset_from_api(url)&.each { |system_code| system_codes << system_code }
        end
        next
      end

      system_url = include['system']

      if system_url && include['concept']
        include['concept'].each do |code|
          system_codes << { system: system_url, code: code.to_hash['code'] }
        end
        next
      end

      if system_url
        if system_url['http://hl7.org/fhir']
          retrieve_valueset_from_api(system_url)&.each { |vs| system_codes << vs }
        end
        next
      end

      value_set_unevaluated << "#{valueset.url}: system url not provided" unless system_url

      # Exclude if system is provided as Uniform Resource Name "urn:"
      # Exclude filter
      # Exclude only system is provided (e.g. http://loing.org)
      exclusions = config.data['Rule']['ValueSetsDemonstrate']['Exclude']
      if exclusions['URL'] && (system_url['urn'])
        value_set_unevaluated << "#{valueset.url}: unable to handle Uniform Resource Name"
      end

      if exclusions['Filter'] && (system_url && include['filter'])
        value_set_unevaluated << "#{valueset.url}: unable to handle filter"
      end

      if exclusions['SystemOnly'] && (system_url && !include['concept'] && !include['filter'])
        value_set_unevaluated << "#{valueset.url}: unabe to handle SystemOnly"
      end
    end
  else
    value_set_unevaluated << valueset.url
  end
  system_codes.flatten.uniq
end

#extract_valueset_from_response(response) ⇒ Object

rubocop:enable Metrics/CyclomaticComplexity

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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 174

def extract_valueset_from_response(response)
  value_set = JSON.parse(response.body)

  if value_set['compose'] && value_set['compose']['include']
    value_set['compose']['include'].map do |include|
      include['concept']&.map { |concept| { system: include['system'], code: concept['code'] } }
    end.flatten
  else
    puts 'No Value Set found in the response.'
  end
end

#resource_uses_code(resource, system, code) ⇒ Object

rubocop:disable Metrics/CyclomaticComplexity

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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 156

def resource_uses_code(resource, system, code)
  resource.each do |key, value|
    next unless key == 'code' || ['value', 'valueCodeableConcept', 'valueString',
                                  'valueQuantity', 'valueBoolean',
                                  'valueInteger', 'valueRange', 'valueRatio',
                                  'valueSampleData', 'valueDateTime',
                                  'valuePeriod', 'valueTime'].include?(key)
    next unless value.is_a?(Hash)

    value['coding']&.each do |codeset|
      return true if codeset.to_hash['system'] == system && codeset.to_hash['code'] == code
    end
  end

  false
end

#retrieve_valueset_from_api(url) ⇒ Object

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# File 'lib/inferno/dsl/fhir_evaluation/rules/value_sets_demonstrate.rb', line 186

def retrieve_valueset_from_api(url)
  url['http:'] = 'https:' if url['http:']
  uri = URI.parse(url)

  http = Net::HTTP.new(uri.host, uri.port)
  http.use_ssl = (uri.scheme == 'https')

  request = Net::HTTP::Get.new(uri.request_uri)

  username = config.data['Environment']['VSAC']['Username']
  password = config.data['Environment']['VSAC']['Password']
  encoded_credentials = Base64.strict_encode64("#{username}:#{password}")
  request['Authorization'] = "Basic #{encoded_credentials}"

  response = http.request(request)

  content_type = response['content-type']
  return unless content_type && !content_type.include?('text/html')

  while response.is_a?(Net::HTTPRedirection)
    redirect_url = response['location']

    redirect_url['xml'] = 'json'
    uri = URI.parse(redirect_url)

    http = Net::HTTP.new(uri.host, uri.port)
    http.use_ssl = (uri.scheme == 'https')

    response = http.request(Net::HTTP::Get.new(uri.request_uri))
  end

  if response.code.to_i == 200
    extract_valueset_from_response(response)
  else
    unless config.data['Rule']['ValueSetsDemonstrate']['IgnoreUnloadableValueset']
      raise StandardError, "Failed to retrieve external value set: #{url} HTTP Status code: #{response.code}"
    end

    value_set_unevaluated << "#{url}: Failed to retrieve. HTTP Status code: #{response.code}"
    nil

  end
end