us_core_test_kit 0.1.0

data/lib/us_core_test_kit/generated/us_core_test_suite.rb

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+require 'inferno/dsl/oauth_credentials'
+require_relative '../version'
+require_relative '../custom_groups/capability_statement_group'
+require_relative '../custom_groups/clinical_notes_guidance_group'
+require_relative '../custom_groups/data_absent_reason_group'
+require_relative 'patient_group'
+require_relative 'allergy_intolerance_group'
+require_relative 'care_plan_group'
+require_relative 'care_team_group'
+require_relative 'condition_group'
+require_relative 'device_group'
+require_relative 'diagnostic_report_note_group'
+require_relative 'diagnostic_report_lab_group'
+require_relative 'document_reference_group'
+require_relative 'goal_group'
+require_relative 'immunization_group'
+require_relative 'medication_request_group'
+require_relative 'smokingstatus_group'
+require_relative 'pediatric_weight_for_height_group'
+require_relative 'observation_lab_group'
+require_relative 'pediatric_bmi_for_age_group'
+require_relative 'pulse_oximetry_group'
+require_relative 'head_circumference_group'
+require_relative 'bodyheight_group'
+require_relative 'bodytemp_group'
+require_relative 'bp_group'
+require_relative 'bodyweight_group'
+require_relative 'heartrate_group'
+require_relative 'resprate_group'
+require_relative 'procedure_group'
+require_relative 'encounter_group'
+require_relative 'organization_group'
+require_relative 'practitioner_group'
+require_relative 'provenance_group'
+
+module USCoreTestKit
+  class USCoreTestSuite < Inferno::TestSuite
+    title 'US Core 3.1.1'
+    version VERSION
+
+    VALIDATION_MESSAGE_FILTERS = [
+      %r{Sub-extension url 'introspect' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris$},
+      %r{Sub-extension url 'revoke' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris$},
+      /^Observation\.effective\.ofType\(Period\): vs-1:/, # Invalid invariant in FHIR v4.0.1
+      /^Observation\.effective\.ofType\(Period\): us-core-1:/ # Invalid invariant in US Core v3.1.1
+    ].freeze
+
+    def self.metadata
+      @metadata ||= YAML.load_file(File.join(__dir__, 'metadata.yml'))[:groups].map do |raw_metadata|
+          Generator::GroupMetadata.new(raw_metadata)
+        end
+    end
+
+    validator do
+      url ENV.fetch('VALIDATOR_URL', 'http://validator_service:4567')
+      exclude_message do |message|
+        VALIDATION_MESSAGE_FILTERS.any? { |filter| filter.match? message.message }
+      end
+    end
+
+    id :us_core_311
+
+    input :url,
+      title: 'FHIR Endpoint',
+      description: 'URL of the FHIR endpoint'
+    input :smart_credentials,
+      title: 'OAuth Credentials',
+      type: :oauth_credentials,
+      optional: true
+
+    fhir_client do
+      url :url
+      oauth_credentials :smart_credentials
+    end
+
+    group from: :us_core_311_capability_statement
+
+    group from: :us_core_311_patient
+    group from: :us_core_311_allergy_intolerance
+    group from: :us_core_311_care_plan
+    group from: :us_core_311_care_team
+    group from: :us_core_311_condition
+    group from: :us_core_311_device
+    group from: :us_core_311_diagnostic_report_note
+    group from: :us_core_311_diagnostic_report_lab
+    group from: :us_core_311_document_reference
+    group from: :us_core_311_goal
+    group from: :us_core_311_immunization
+    group from: :us_core_311_medication_request
+    group from: :us_core_311_smokingstatus
+    group from: :us_core_311_pediatric_weight_for_height
+    group from: :us_core_311_observation_lab
+    group from: :us_core_311_pediatric_bmi_for_age
+    group from: :us_core_311_pulse_oximetry
+    group from: :us_core_311_head_circumference
+    group from: :us_core_311_bodyheight
+    group from: :us_core_311_bodytemp
+    group from: :us_core_311_bp
+    group from: :us_core_311_bodyweight
+    group from: :us_core_311_heartrate
+    group from: :us_core_311_resprate
+    group from: :us_core_311_procedure
+    group from: :us_core_311_encounter
+    group from: :us_core_311_organization
+    group from: :us_core_311_practitioner
+    group from: :us_core_311_provenance
+    group from: :us_core_311_clinical_notes_guidance
+    group from: :us_core_311_data_absent_reason
+  end
+end

data/lib/us_core_test_kit/generator/group_generator.rb

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+require_relative 'naming'
+require_relative 'special_cases'
+
+module USCoreTestKit
+  class Generator
+    class GroupGenerator
+      class << self
+        def generate(ig_metadata)
+          ig_metadata.ordered_groups
+            .reject { |group| SpecialCases.exclude_resource? group.resource }
+            .each { |group| new(group).generate }
+        end
+      end
+
+      attr_accessor :group_metadata
+
+      def initialize(group_metadata)
+        self.group_metadata = group_metadata
+      end
+
+      def template
+        @template ||= File.read(File.join(__dir__, 'templates', 'group.rb.erb'))
+      end
+
+      def output
+        @output ||= ERB.new(template).result(binding)
+      end
+
+      def base_output_file_name
+        "#{class_name.underscore}.rb"
+      end
+
+      def base_metadata_file_name
+        "metadata.yml"
+      end
+
+      def class_name
+        "#{Naming.upper_camel_case_for_profile(group_metadata)}Group"
+      end
+
+      def title
+        group_metadata.title
+      end
+
+      def short_description
+        group_metadata.short_description
+      end
+
+      def output_file_name
+        File.join(__dir__, '..', 'generated', base_output_file_name)
+      end
+
+      def metadata_file_name
+        File.join(__dir__, '..', 'generated', profile_identifier, base_metadata_file_name)
+      end
+
+      def profile_identifier
+        Naming.snake_case_for_profile(group_metadata)
+      end
+
+      def group_id
+        "us_core_311_#{profile_identifier}"
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def profile_name
+        group_metadata.profile_name
+      end
+
+      def profile_url
+        group_metadata.profile_url
+      end
+
+      def generate
+        File.open(output_file_name, 'w') { |f| f.write(output) }
+        group_metadata.id = group_id
+        group_metadata.file_name = base_output_file_name
+        File.open(metadata_file_name, 'w') { |f| f.write(YAML.dump(group_metadata.to_hash)) }
+      end
+
+      def test_id_list
+        @test_id_list ||=
+          group_metadata.tests.map { |test| test[:id] }
+      end
+
+      def test_file_list
+        @test_file_list ||=
+          group_metadata.tests.map { |test| test[:file_name].delete_suffix('.rb') }
+      end
+
+      def required_searches
+        group_metadata.searches.select { |search| search[:expectation] == 'SHALL' }
+      end
+
+      def search_param_name_string
+        required_searches
+          .map { |search| search[:names].join(' + ') }
+          .map { |names| "* #{names}" }
+          .join("\n")
+      end
+
+      def search_description
+        return '' if required_searches.blank?
+
+        <<~SEARCH_DESCRIPTION
+        ## Searching
+        This test sequence will first perform each required search associated
+        with this resource. This sequence will perform searches with the
+        following parameters:
+
+        #{search_param_name_string}
+
+        ### Search Parameters
+        The first search uses the selected patient(s) from the prior launch
+        sequence. Any subsequent searches will look for its parameter values
+        from the results of the first search. For example, the `identifier`
+        search in the patient sequence is performed by looking for an existing
+        `Patient.identifier` from any of the resources returned in the `_id`
+        search. If a value cannot be found this way, the search is skipped.
+
+        ### Search Validation
+        Inferno will retrieve up to the first 20 bundle pages of the reply for
+        #{resource_type} resources and save them for subsequent tests. Each of
+        these resources is then checked to see if it matches the searched
+        parameters in accordance with [FHIR search
+        guidelines](https://www.hl7.org/fhir/search.html). The test will fail,
+        for example, if a Patient search for `gender=male` returns a `female`
+        patient.
+        SEARCH_DESCRIPTION
+      end
+
+      def description
+        <<~DESCRIPTION
+        # Background
+
+        The US Core #{title} sequence verifies that the system under test is
+        able to provide correct responses for #{resource_type} queries. These queries
+        must contain resources conforming to the #{profile_name} as
+        specified in the US Core v3.1.1 Implementation Guide.
+
+        # Testing Methodology
+        #{search_description}
+
+        ## Must Support
+        Each profile contains elements marked as "must support". This test
+        sequence expects to see each of these elements at least once. If at
+        least one cannot be found, the test will fail. The test will look
+        through the #{resource_type} resources found in the first test for these
+        elements.
+
+        ## Profile Validation
+        Each resource returned from the first search is expected to conform to
+        the [#{profile_name}](#{profile_url}). Each element is checked against
+        teminology binding and cardinality requirements.
+
+        Elements with a required binding are validated against their bound
+        ValueSet. If the code/system in the element is not part of the ValueSet,
+        then the test will fail.
+
+        ## Reference Validation
+        Each reference within the resources found from the previous tests must
+        resolve. The test will attempt to read each reference found and will
+        fail if any attempted read fails.
+        DESCRIPTION
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/group_metadata.rb

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+module USCoreTestKit
+  class Generator
+    class GroupMetadata
+      ATTRIBUTES = [
+        :name,
+        :class_name,
+        :version,
+        :reformatted_version,
+        :resource,
+        :profile_url,
+        :profile_name,
+        :title,
+        :short_description,
+        :interactions,
+        :operations,
+        :searches,
+        :search_definitions,
+        :include_params,
+        :revincludes,
+        :required_concepts,
+        :must_supports,
+        :mandatory_elements,
+        :bindings,
+        :references,
+        :tests,
+        :id,
+        :file_name,
+        :delayed_references
+      ].freeze
+
+      NON_USCDI_RESOURCES = [
+        'Encounter',
+        'Location',
+        'Organization',
+        'Practitioner',
+        'PractitionerRole',
+        'Provenance'
+      ].freeze
+
+      ATTRIBUTES.each { |name| attr_accessor name }
+
+      def initialize(**params)
+        params.each do |key, value|
+          raise "Unknown attribute #{key}" unless ATTRIBUTES.include? key
+
+          instance_variable_set(:"@#{key}", value)
+        end
+      end
+
+      def delayed?
+        return false if resource == 'Patient'
+
+        no_patient_searches? || non_uscdi_resource?
+      end
+
+      def no_patient_searches?
+        searches.none? { |search| search[:names].include? 'patient' }
+      end
+
+      def non_uscdi_resource?
+        NON_USCDI_RESOURCES.include? resource
+      end
+
+      def add_test(id:, file_name:)
+        self.tests ||= []
+
+        test_metadata = {
+          id: id,
+          file_name: file_name
+        }
+
+        if delayed? && id.include?('read')
+          self.tests.unshift(test_metadata)
+        else
+          self.tests << test_metadata
+        end
+      end
+
+      def to_hash
+        ATTRIBUTES.each_with_object({}) { |key, hash| hash[key] = send(key) }
+      end
+
+      def add_delayed_references(delayed_profiles, ig_resources)
+        self.delayed_references =
+          references
+            .select { |reference| (reference[:profiles] & delayed_profiles).present? }
+            .map do |reference|
+              profile_urls = (reference[:profiles] & delayed_profiles)
+              delayed_resources = profile_urls.map { |url| ig_resources.resource_for_profile(url) }
+              {
+                path: reference[:path].gsub("#{resource}.", ''),
+                resources: delayed_resources
+              }
+            end
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/group_metadata_extractor.rb

@@ -0,0 +1,281 @@
+require_relative 'group_metadata'
+require_relative 'ig_metadata'
+require_relative 'must_support_metadata_extractor'
+require_relative 'search_metadata_extractor'
+require_relative 'terminology_binding_metadata_extractor'
+
+module USCoreTestKit
+  class Generator
+    class GroupMetadataExtractor
+      attr_accessor :resource_capabilities, :profile_url, :ig_metadata, :ig_resources
+
+      def initialize(resource_capabilities, profile_url, ig_metadata, ig_resources)
+        self.resource_capabilities = resource_capabilities
+        self.profile_url = profile_url
+        self.ig_metadata = ig_metadata
+        self.ig_resources = ig_resources
+      end
+
+      def group_metadata
+        @group_metadata ||=
+          GroupMetadata.new(group_metadata_hash)
+      end
+
+      def group_metadata_hash
+        @group_metadata_hash ||=
+          {
+            name: name,
+            class_name: class_name,
+            version: version,
+            reformatted_version: reformatted_version,
+            # test_id_prefix: test_id_prefix,
+            resource: resource,
+            profile_url: profile_url,
+            profile_name: profile_name,
+            title: title,
+            short_description: short_description,
+            interactions: interactions,
+            operations: operations,
+            searches: searches,
+            search_definitions: search_definitions,
+            include_params: include_params,
+            revincludes: revincludes,
+            required_concepts: required_concepts,
+            must_supports: must_supports,
+            mandatory_elements: mandatory_elements,
+            bindings: bindings,
+            references: references
+            # tests: []
+          }
+
+        mark_mandatory_and_must_support_searches
+        handle_special_cases
+
+        @group_metadata_hash
+      end
+
+      def mark_mandatory_and_must_support_searches
+        searches.each do |search|
+          search[:names_not_must_support_or_mandatory] = search[:names].reject do |name|
+            path = search_definitions[name.to_sym][:full_path]
+            any_must_support_elements = (must_supports[:elements]).any? do |element|
+              full_must_support_path = "#{resource}.#{element[:path]}"
+
+              # allow for non-choice, choice types, and _id
+              name == '_id' || full_must_support_path == path || full_must_support_path == "#{path}[x]"
+            end
+
+            any_must_support_slices = must_supports[:slices].any? do |slice|
+              # only handle type slices because that is all we need for now
+              if slice[:discriminator] && slice[:discriminator][:type] == 'type'
+                full_must_support_path = "#{resource}.#{slice[:path].sub('[x]', slice[:discriminator][:code])}"
+                full_must_support_path == path
+              else
+                false
+              end
+            end
+
+            any_mandatory_elements = mandatory_elements.any? do |element|
+              element == path
+            end
+
+            any_must_support_elements || any_must_support_slices || any_mandatory_elements
+          end
+
+          search[:must_support_or_mandatory] = search[:names_not_must_support_or_mandatory].empty?
+        end
+      end
+
+      ### BEGIN SPECIAL CASES ###
+
+      CATEGORY_FIRST_PROFILES = [
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-lab',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note'
+      ]
+
+      def category_first_profile?
+        CATEGORY_FIRST_PROFILES.include?(profile_url)
+      end
+
+      def first_search_params
+        @first_search_params ||=
+        if category_first_profile?
+          ['patient', 'category']
+        elsif resource == 'Observation'
+          ['patient', 'code']
+        elsif resource == 'MedicationRequest'
+          ['patient', 'intent']
+        else
+          ['patient']
+        end
+      end
+
+      def handle_special_cases
+        set_first_search
+
+        case profile_url
+        when 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-implantable-device'
+          must_supports[:elements].delete_if do |element|
+            ['udiCarrier.carrierAIDC', 'udiCarrier.carrierHRF'].include? element[:path]
+          end
+        when 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference'
+          must_supports[:elements].delete_if do |element|
+            ['content.attachment.data', 'content.attachment.url'].include? element[:path]
+          end
+        end
+      end
+
+      def set_first_search
+        search = searches.find { |param| param[:names] == first_search_params }
+        return if search.nil?
+
+        searches.delete(search)
+        searches.unshift(search)
+      end
+
+      ### END SPECIAL CASES ###
+
+      def profile
+        @profile ||= ig_resources.profile_by_url(profile_url)
+      end
+
+      def profile_elements
+        @profile_elements ||= profile.snapshot.element
+      end
+
+      def base_name
+        profile_url.split('StructureDefinition/').last
+      end
+
+      def name
+        base_name.tr('-', '_')
+      end
+
+      def class_name
+        base_name
+          .split('-')
+          .map(&:capitalize)
+          .join
+          .gsub('UsCore', "USCore#{ig_metadata.reformatted_version}")
+          .concat('Sequence')
+      end
+
+      def version
+        ig_metadata.ig_version
+      end
+
+      def reformatted_version
+        ig_metadata.reformatted_version
+      end
+
+      def resource
+        resource_capabilities.type
+      end
+
+      def profile_name
+        profile.title.gsub('  ', ' ')
+      end
+
+      def title
+        profile.title.gsub(/US\s*Core\s*/, '').gsub(/\s*Profile/, '').strip
+      end
+
+      def short_description
+        "Verify support for the server capabilities required by the #{profile_name}."
+      end
+
+      def interactions
+        @interactions ||=
+          resource_capabilities.interaction.map do |interaction|
+            {
+              code: interaction.code,
+              expectation: interaction.extension.first.valueCode # TODO: fix expectation extension finding
+            }
+          end
+      end
+
+      def operations
+        @operations ||=
+          resource_capabilities.operation.map do |operation|
+            {
+              code: operation.name,
+              expectation: operation.extension.first.valueCode # TODO: fix expectation extension finding
+            }
+          end
+      end
+
+      def search_metadata_extractor
+        @search_metadata_extractor ||=
+          SearchMetadataExtractor.new(resource_capabilities, ig_resources, resource, profile_elements)
+      end
+
+      def searches
+        @searches ||= search_metadata_extractor.searches
+      end
+
+      def search_definitions
+        @search_definitions ||= search_metadata_extractor.search_definitions
+      end
+
+      def include_params
+        resource_capabilities.searchInclude || []
+      end
+
+      def revincludes
+        resource_capabilities.searchRevInclude || []
+      end
+
+      def required_concepts
+        # The base FHIR vital signs profile has a required binding that isn't
+        # relevant for any of its child profiles
+        return if resource == 'Observation'
+
+        profile_elements
+          .select { |element| element.type&.any? { |type| type.code == 'CodeableConcept' } }
+          .select { |element| element.binding&.strength == 'required' }
+          .map { |element| element.path.gsub("#{resource}.", '').gsub('[x]', 'CodeableConcept') }
+      end
+
+      def terminology_binding_metadata_extractor
+        @terminology_binding_metadata_extractor ||=
+          TerminologyBindingMetadataExtractor.new(profile_elements, ig_resources, resource)
+      end
+
+      def bindings
+        @bindings ||=
+          terminology_binding_metadata_extractor.terminology_bindings
+      end
+
+      def must_support_metadata_extractor
+        @must_support_metadata_extractor ||=
+          MustSupportMetadataExtractor.new(profile_elements, profile, resource)
+      end
+
+      def must_supports
+        @must_supports ||=
+          must_support_metadata_extractor.must_supports
+      end
+
+      def mandatory_elements
+        @mandatory_elements ||=
+          profile_elements
+            .select { |element| element.min.positive? }
+            .map { |element| element.path }
+      end
+
+      def references
+        @references ||=
+          profile_elements
+            .select { |element| element.type&.first&.code == 'Reference' }
+            .map do |reference_definition|
+              {
+                path: reference_definition.path,
+                profiles: reference_definition.type.first.targetProfile
+              }
+            end
+      end
+    end
+  end
+end