Module: DaVinciDTRTestKit::CQLTest

Included in:
DTRCustomQuestionnaireExpressionsTest, DTRCustomQuestionnaireExtensionsTest, DTRCustomQuestionnaireLibrariesTest, DTRCustomQuestionnairePackageValidationTest, DTRQuestionnaireMustSupportTes, DTRQuestionnaireResponseValidation, PayerAdaptiveFormExpressionsTest, PayerAdaptiveFormExtensionsTest, PayerAdaptiveFormLibrariesTest, PayerAdaptiveFormQuestionnaireResponseTest, PayerAdaptiveNexQuestionExtensionsTest, PayerAdaptiveNextQuestionExpressionsTest, PayerStaticFormExpressionsTest, PayerStaticFormExtensionsTest, PayerStaticFormLibrariesTest, PayerStaticFormResponseTest
Defined in:
lib/davinci_dtr_test_kit/cql_test.rb

Constant Summary collapse

STATIC_QUESTIONNAIRE_PACKAGE_BUNDLE_PROFILE = 
'http://hl7.org/fhir/us/davinci-dtr/StructureDefinition/DTR-QPackageBundle|2.0.1'.freeze
STATIC_QUESTIONNAIRE_PACKAGE_PARAMETER_PROFILE = 
'http://hl7.org/fhir/us/davinci-dtr/StructureDefinition/dtr-qpackage-output-parameters|2.0.1'.freeze
ADAPTIVE_QUESTIONNAIRE_PACKAGE_BUNDLE_PROFILE = 
'http://hl7.org/fhir/us/davinci-dtr/StructureDefinition/DTR-QPackageBundle|2.0.1'.freeze
ADAPTIVE_QUESTIONNAIRE_PACKAGE_PARAMETER_PROFILE = 
'http://hl7.org/fhir/us/davinci-dtr/StructureDefinition/dtr-qpackage-output-parameters|2.0.1'.freeze

Instance Method Summary collapse

Instance Method Details

#add_formatting_messages(misformatted_expressions, q_index) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 151

def add_formatting_messages(misformatted_expressions, q_index)
  misformatted_expressions.compact.each do |idx|
    messages << { type: 'info',
                  message: format_markdown("[expression #{idx + 1}] in [questionnaire #{q_index + 1}]
                  does not begin with a reference to an included library name.") }
  end
end

#add_item_messages(found_item_expressions, q_index) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 169

def add_item_messages(found_item_expressions, q_index)
  unless found_item_expressions['found_candidate_expression']
    messages << { type: 'info',
                  message: format_markdown("[questionnaire #{q_index + 1}] included no candidate expression.") }
  end
  unless found_item_expressions['found_init_expression']
    messages << { type: 'info',
                  message: format_markdown("[questionnaire #{q_index + 1}] included no initial expression.") }
  end
  return if found_item_expressions['found_context_expression']

  messages << { type: 'info',
                message: format_markdown("[questionnaire #{q_index + 1}] included no context expression.") }
end

#add_launch_context_messages(found_launch_context, found_variable, found_pop_context, found_cqf_lib, q_index) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 129

def add_launch_context_messages(found_launch_context, found_variable, found_pop_context, found_cqf_lib, q_index)
  unless found_launch_context
    messages << { type: 'info',
                  message: format_markdown("[questionnaire #{q_index + 1}] included no launch context.") }
  end
  unless found_variable
    messages << { type: 'info',
                  message: format_markdown("[questionnaire #{q_index + 1}]
                   included no variable to query for additional data.") }
  end
  unless found_pop_context
    messages << { type: 'info',
                  message: format_markdown("[questionnaire #{q_index + 1}]
                   included no item population context.") }
  end
  return if found_cqf_lib

  messages << { type: 'info',
                message: format_markdown("[questionnaire #{q_index + 1}]
                  included no cqf library.") }
end

#check_expression_format(item_ext, index) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 294

def check_expression_format(item_ext, index)
  return unless library_names.none?

  expression_passes = false
  library_names.each do |name|
    if item_ext.valueExpression.expression.start_with? "\"#{name}\""
      expression_passes = true
      break
    end
  end
  index unless expression_passes
end

#check_for_cql(extension, extension_name, index, q_index, url, link_id = '') ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 307

def check_for_cql(extension, extension_name, index, q_index, url, link_id = '')
  return if extension.valueExpression.nil?
  return if extension.valueExpression.language == 'text/cql'

  cql_presence[extension_name] = false unless extension_name.blank?
  messages << if link_id.blank?
                { type: 'info',
                  message: format_markdown("[extension #{index + 1}] in [questionnaire #{q_index + 1}]
                      contains expression that does not have content type of cql
                      (URL: #{url}).") }
              else
                { type: 'info',
                  message: format_markdown("[item #{index + 1}] in [questionnaire #{q_index + 1}]
                      contains expression that does not have content type of cql
                      (linkId: #{link_id}, URL: #{url}).") }
              end
end

#check_item_extension(item_ext, index, q_index, found_item_expressions, link_id) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 260

def check_item_extension(item_ext, index, q_index, found_item_expressions, link_id)
  if item_ext.url == 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-candidateExpression'
    found_item_expressions['found_candidate_expression'] = true
    extension_presence['found_min_candidate_expression'] = true
    check_for_cql(item_ext, 'candidate_expression', index, q_index, item_ext.url, link_id)
    return check_expression_format(item_ext, index)
  end
  if item_ext.url == 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression'
    found_item_expressions['found_init_expression'] = true
    extension_presence['found_min_init_expression'] = true
    check_for_cql(item_ext, 'init_expression', index, q_index, item_ext.url, link_id)
    return check_expression_format(item_ext, index)
  end
  if item_ext.url == 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-contextExpression'
    found_item_expressions['found_context_expression'] = true
    extension_presence['found_min_context_expression'] = true
    check_for_cql(item_ext, 'context_expression', index, q_index, item_ext.url, link_id)
    return check_expression_format(item_ext, index)
  end
  check_for_cql(item_ext, '', index, q_index, item_ext.url, link_id)
end

#check_libraries(questionnaire_bundles) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 240

def check_libraries(questionnaire_bundles)
  libraries = extract_libraries_from_bundles(questionnaire_bundles)

  assert libraries.any?, 'No Libraries found.'

  libraries.each do |lib|
    library_urls.add(lib.url) unless lib.url.nil?
    evaluate_library(lib)
    library_names.add(lib.name)
  end
end

#check_library_references ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 252

def check_library_references
  missing_references = cqf_reference_libraries.select do |url|
    library_urls.exclude? url
  end
  assert missing_references.empty?,
         "Some libraries referenced by cqf-libraries were not found: #{missing_references.join(', ')}"
end

#check_nested_items(item, index, q_index, found_item_expressions, link_id) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 282

def check_nested_items(item, index, q_index, found_item_expressions, link_id)
  misformatted_nested_expressions = []
  item.item.each do |nested_item|
    check_nested_items(nested_item, index, q_index, found_item_expressions, nested_item.linkId)
    nested_item.extension.each do |item_ext|
      misformatted_nested_expressions << check_item_extension(item_ext, index, q_index, found_item_expressions,
                                                              link_id)
    end
  end
  misformatted_nested_expressions.compact
end

#check_questionnaire_extensions(questionnaire, q_index) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 75

def check_questionnaire_extensions(questionnaire, q_index)
  # are extensions present in this questionnaire?
  found_launch_context = found_variable = found_pop_context = found_cqf_lib = false
  cqf_count = total_cqf_libs(questionnaire.extension)
  misformatted_expressions = []
  questionnaire.extension.each_with_index do |extension, index|
    if extension.url == 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-launchContext'
      found_launch_context = true
      extension_presence['found_min_launch_context'] = true
      check_for_cql(extension, 'launch_context', index, q_index, extension.url)
      misformatted_expressions << check_expression_format(extension, index)
    end
    if extension.url == 'http://hl7.org/fhir/StructureDefinition/variable'
      found_variable = true
      extension_presence['found_min_variable'] = true
      check_for_cql(extension, 'variable', index, q_index, extension.url)
      misformatted_expressions << check_expression_format(extension, index)
    end
    if extension.url == 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemPopulationContext'
      found_pop_context = true
      extension_presence['found_min_pop_context'] = true
      check_for_cql(extension, 'pop_context', index, q_index, extension.url)
      misformatted_expressions << check_expression_format(extension, index)
    end
    next unless extension.url == 'http://hl7.org/fhir/StructureDefinition/cqf-library'

    cqf_reference_libraries.add(extension.valueCanonical)
    found_cqf_lib = true
    extension_presence['found_min_cqf_lib'] = true

    check_for_cql(extension, '', index, q_index, extension.url)
  end
  add_launch_context_messages(found_launch_context, found_variable, found_pop_context, found_cqf_lib, q_index)
  return if cqf_count < 1

  add_formatting_messages(misformatted_expressions, q_index)
  assert misformatted_expressions.compact.empty?, 'Expression in questionnaire misformatted.'
end

#check_questionnaire_items(questionnaire, q_index) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 184

def check_questionnaire_items(questionnaire, q_index)
  # are expressions present in this questionnaire?
  found_item_expressions = { 'found_init_expression' => false,
                             'found_candidate_expression' => false,
                             'found_context_expression' => false }
  cqf_count = total_cqf_libs(questionnaire.extension)
  misformatted_expressions = []

  # check questionnaire items
  questionnaire.item.each_with_index do |item, index|
    misformatted_expressions.concat(check_nested_items(item, index, q_index, found_item_expressions, item.linkId))
    # check extensions on items
    item.extension.each do |item_ext|
      misformatted_expressions << check_item_extension(item_ext,
                                                       index, q_index, found_item_expressions, item.linkId)
    end
  end
  add_item_messages(found_item_expressions, q_index)
  # only care about formatting when there are multiple cqf libs
  return if cqf_count < 1

  misformatted_expressions.compact.to_set.each do |idx|
    messages << { type: 'info',
                  message: format_markdown("[item #{idx + 1}] in [questionnaire #{q_index + 1}]
                  contains expression that does not begin with a reference to an included library name.") }
  end
  assert misformatted_expressions.compact.to_set.empty?, 'Expression in questionnaire misformatted.'
end

#cqf_reference_libraries ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 30

def cqf_reference_libraries
  scratch[:cqf_reference_libraries] ||= Set.new
end

#cql_presence ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 24

def cql_presence
  @cql_presence ||= { 'launch_context' => true, 'variable' => true,
                      'pop_context' => true, 'init_expression' => true,
                      'candidate_expression' => true, 'context_expression' => true }
end

#evaluate_library(library) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 213

def evaluate_library(library)
  found_cql = found_elm = false
  library.content.each do |content|
    if content.data.nil?
      messages << { type: 'info',
                    message: format_markdown("[library #{library.url}] content element included no data.") }
    end
    if content.contentType == 'text/cql'
      found_cql = true
    elsif content.contentType == 'application/elm+json'
      found_elm = true
    else
      messages << { type: 'info',
                    message: format_markdown("[library #{library.url}] has non-cql/elm content.") }
      true
    end
    next unless library_names.include? library.name

    found_duplicate_library_name = true
    messages << { type: 'info', message: format_markdown("[library #{library.url}] has a name,
     #{library.name}, that is already included in the bundle.") }
    assert !found_duplicate_library_name, 'Found duplicate library names - all names must be unique.'
  end
  assert found_cql, "[library #{library.url}] does not include CQL."
  assert found_elm, "[library #{library.url}] does not include ELM."
end

#extension_presence ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 17

def extension_presence
  @extension_presence ||= { 'found_min_launch_context' => false, 'found_min_variable' => false,
                            'found_min_pop_context' => false, 'found_min_init_expression' => false,
                            'found_min_candidate_expression' => false, 'found_min_context_expression' => false,
                            'found_min_cqf_lib' => false }
end

#extract_bundles_from_parameter(parameter) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 365

def extract_bundles_from_parameter(parameter)
  return [] if parameter.blank?

  parameter.parameter&.filter_map do |param|
    param.resource if param.resource&.resourceType == 'Bundle'
  end
end

#extract_contained_questionnaires(questionnaire_responses) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 325

def extract_contained_questionnaires(questionnaire_responses)
  questionnaire_responses&.filter_map do |qr|
    qr.contained&.filter { |resource| resource.is_a?(FHIR::Questionnaire) }
  end&.flatten&.compact
end

#extract_libraries_from_bundles(questionnaire_bundles) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 381

def extract_libraries_from_bundles(questionnaire_bundles)
  questionnaire_bundles.filter_map do |qb|
    qb.entry.filter_map { |entry| entry.resource if entry&.resource.is_a?(FHIR::Library) }
  end&.flatten&.compact
end

#extract_questionnaire_bundles(resource) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 354

def extract_questionnaire_bundles(resource)
  case resource&.resourceType
  when 'Bundle'
    [resource]
  when 'Parameters'
    extract_bundles_from_parameter(resource)
  else
    []
  end
end

#extract_questionnaire_from_questionnaire_package(questionnaire_pkg_json, questionnaire_url) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 373

def extract_questionnaire_from_questionnaire_package(questionnaire_pkg_json, questionnaire_url)
  resource = FHIR.from_contents(questionnaire_pkg_json)
  questionnaire_bundles = extract_questionnaire_bundles(resource)
  questionnaires = extract_questionnaires_from_bundles(questionnaire_bundles)

  questionnaires.find { |q| q.url == questionnaire_url }
end

#extract_questionnaires_from_bundles(questionnaire_bundles) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 331

def extract_questionnaires_from_bundles(questionnaire_bundles)
  questionnaire_bundles.filter_map do |qb|
    qb.entry.filter_map { |entry| entry.resource if entry.resource.is_a?(FHIR::Questionnaire) }
  end&.flatten&.compact
end

#found_duplicate_library_name ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 46

def found_duplicate_library_name
  @found_duplicate_library_name ||= false
end

#found_non_cql_elm_library ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 50

def found_non_cql_elm_library
  @found_non_cql_elm_library ||= false
end

#found_non_cql_expression ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 54

def found_non_cql_expression
  @found_non_cql_expression ||= false
end

#found_questionnaire ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 42

def found_questionnaire
  @found_questionnaire ||= false
end

#library_names ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 38

def library_names
  scratch[:library_names] ||= Set.new
end

#library_urls ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 34

def library_urls
  scratch[:library_urls] ||= Set.new
end

#perform_questionnaire_package_validation(resource, form = 'static') ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 337

def perform_questionnaire_package_validation(resource, form = 'static')
  scratch[:"#{form}_questionnaire_bundles"] = extract_questionnaire_bundles(resource)
  validate_questionnaire_package(resource, form)
  assert scratch[:"#{form}_questionnaire_bundles"].present?, 'No questionnaire bundle found in the response'
end

#questionnaire_package_profile_urls ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 8

def questionnaire_package_profile_urls
  {
    static_bundle: STATIC_QUESTIONNAIRE_PACKAGE_BUNDLE_PROFILE,
    static_parameter: STATIC_QUESTIONNAIRE_PACKAGE_PARAMETER_PROFILE,
    adaptive_bundle: ADAPTIVE_QUESTIONNAIRE_PACKAGE_BUNDLE_PROFILE,
    adaptive_parameter: ADAPTIVE_QUESTIONNAIRE_PACKAGE_PARAMETER_PROFILE
  }
end

#reset_cql_tests ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 58

def reset_cql_tests
  library_names.clear
  library_urls.clear
  cqf_reference_libraries.clear
  extension_presence.each_key { |k| extension_presence[k] = false }
end

#total_cqf_libs(extensions) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 159

def total_cqf_libs(extensions)
  cqf_count = 0
  extensions.each do |extension|
    next unless extension.url == 'http://hl7.org/fhir/StructureDefinition/cqf-library'

    cqf_count += 1
  end
  cqf_count
end

#validate_questionnaire_package(resource, form) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 343

def validate_questionnaire_package(resource, form)
  case resource&.resourceType
  when 'Bundle'
    assert_valid_resource(resource:, profile_url: questionnaire_package_profile_urls[:"#{form}_bundle"])
  when 'Parameters'
    assert_valid_resource(resource:, profile_url: questionnaire_package_profile_urls[:"#{form}_parameter"])
  else
    assert(false, "Unexpected resourceType: #{resource&.resourceType}. Expected Parameters or Bundle")
  end
end

#verify_questionnaire_extensions(questionnaires) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 65

def verify_questionnaire_extensions(questionnaires)
  assert questionnaires&.any? && questionnaires.all? { |q| q.is_a? FHIR::Questionnaire }, 'No questionnaires found.'
  questionnaires.each_with_index { |q, q_index| check_questionnaire_extensions(q, q_index) }
  check_library_references
  assert extension_presence.value?(true), 'No extensions found. Questionnaire must demonstrate prepopulation.'
  assert cql_presence['variable'], 'Variable expression logic not written in CQL.'
  assert cql_presence['launch_context'], 'Launch context expression logic not written in CQL.'
  assert cql_presence['pop_context'], 'Population context expression logic not written in CQL.'
end

#verify_questionnaire_items(questionnaires, final_cql_test: false) ⇒ Object 



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# File 'lib/davinci_dtr_test_kit/cql_test.rb', line 114

def verify_questionnaire_items(questionnaires, final_cql_test: false)
  assert questionnaires&.any? && questionnaires.all? { |q| q.is_a? FHIR::Questionnaire }, 'No questionnaires found.'
  questionnaires.each_with_index { |q, q_index| check_questionnaire_items(q, q_index) }

  begin
    assert !found_non_cql_expression, 'Found non-cql expression.'
    assert extension_presence.value?(true), 'No extensions found. Questionnaire must demonstrate prepopulation.'
    assert cql_presence['init_expression'], 'Initial expression logic not written in CQL.'
    assert cql_presence['candidate_expression'], 'Candidate expression logic not written in CQL.'
    assert cql_presence['context_expression'], 'Context expression logic not written in CQL.'
  ensure
    reset_cql_tests if final_cql_test
  end
end