au_core_test_kit 0.0.16

data/lib/au_core_test_kit/custom_groups/clinical_note_type_test.rb

@@ -0,0 +1,114 @@
+# frozen_string_literal: true
+
+require_relative '../search_test'
+
+module AUCoreTestKit
+  class ClinicalNoteTypeTest < Inferno::Test
+    include SearchTest
+
+    id :au_core_clinical_note_types
+    title 'Server demonstrates support for the required DocumentReference types and DiagnosticReport categories.'
+
+    input :patient_ids,
+          title: 'Patient IDs',
+          description: 'Comma separated list of patient IDs that in sum contain all MUST SUPPORT elements'
+
+    REQUIRED_CATEGORIES = %w[LP29708-2 LP7839-6 LP29684-5].freeze
+
+    def document_reference_types_found(patient_id)
+      search_params = { patient: patient_id }
+      status_values = ['current,superseded,entered-in-error']
+
+      search_and_check_response(search_params, 'DocumentReference')
+
+      if response[:status] == 400
+        perform_search_with_status(
+          params,
+          patient_id,
+          status_search_values: status_values,
+          resource_type: 'DocumentReference'
+        )
+      end
+
+      resources = fetch_all_bundled_resources(resource_type: 'DocumentReference')
+                  .select { |resource| resource.resourceType == 'DocumentReference' }
+
+      scratch[:document_reference_attachments] ||= {}
+      scratch[:document_reference_attachments][patient_id] ||= {}
+      attachments = scratch[:document_reference_attachments][patient_id]
+
+      codes_found =
+        resources.flat_map do |resource|
+          resource.content
+                  &.select { |content| content.attachment&.url.present? && !attachments.key?(content.attachment&.url) }
+                  &.each { |content| attachments[content.attachment.url] = resource.id }
+
+          resource.type&.coding&.map(&:code)
+        end
+
+      codes_found.compact.uniq
+    end
+
+    def diagnostic_report_categories_found(patient_id)
+      search_params = { patient: patient_id }
+      status_values = ['registered,partial,preliminary,final,amended,corrected,appended,cancelled,entered-in-error,unknown']
+      search_and_check_response(search_params, 'DiagnosticReport')
+
+      if response[:status] == 400
+        perform_search_with_status(
+          params,
+          patient_id,
+          status_search_values: status_values,
+          resource_type: 'DiagnosticReport'
+        )
+      end
+
+      resources = fetch_all_bundled_resources(resource_type: 'DiagnosticReport')
+                  .select { |resource| resource.resourceType == 'DiagnosticReport' }
+
+      scratch[:diagnostic_report_attachments] ||= {}
+      scratch[:diagnostic_report_attachments][patient_id] ||= {}
+      attachments = scratch[:diagnostic_report_attachments][patient_id]
+
+      codes_found =
+        resources.flat_map do |resource|
+          codes = resource.category&.flat_map do |category|
+            category.coding&.map { |coding| coding.code if REQUIRED_CATEGORIES.include?(coding.code) }
+          end&.compact
+
+          if codes.present?
+            resource.presentedForm
+                    &.select { |attachment| attachment&.url.present? && !attachments.key?(attachment&.url) }
+                    &.each { |attachment| attachments[attachment.url] = resource.id }
+          end
+
+          codes
+        end
+
+      codes_found.compact.uniq
+    end
+
+    run do
+      missing_types = config.options[:required_types].dup
+      missing_categories = REQUIRED_CATEGORIES.dup
+
+      patient_id_list.each do |patient_id|
+        missing_types -= document_reference_types_found(patient_id)
+        missing_categories -= diagnostic_report_categories_found(patient_id)
+      end
+
+      pass if missing_types.empty? && missing_categories.empty?
+
+      message = 'Could not find these '
+
+      if missing_types.present?
+        message += "DocumentReference types: #{missing_types.join(', ')}"
+        message += ' and ' if missing_categories.present?
+      end
+
+      message += "DiagnosticReport categories #{missing_categories.join(', ')}." if missing_categories.present?
+
+      skip message
+    end
+  end
+end

data/lib/au_core_test_kit/custom_groups/missing_data_group.rb

@@ -0,0 +1,88 @@
+# frozen_string_literal: true
+
+require_relative '../helpers'
+
+module AUCoreTestKit
+  module AUCoreV100
+    class MissingDataGroup < Inferno::TestGroup
+      RESOURCE_PROFILES = %w[
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-allergyintolerance
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-condition
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-encounter
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-immunization
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-location
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-medicationrequest
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-organization
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-patient
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-practitioner
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-practitionerrole
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-procedure
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-bodyweight
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-bloodpressure
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-bodyheight
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult-path
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-bodytemp
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-heartrate
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-waistcircum
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-resprate
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult
+        http://hl7.org.au/fhir/core/StructureDefinition/au-core-smokingstatus
+      ].freeze
+
+      id :au_core_missing_data_group
+      title 'Missing Data Tests'
+      short_description 'Verify that the server is capable of representing missing data.'
+      description %(
+        The [AU Core Missing Data
+        Guidance](https://build.fhir.org/ig/hl7au/au-fhir-core/general-requirements.html#missing-data)
+        gives instructions on how to represent various types of missing data.
+
+        In the previous resource tests, each resource returned from the server was
+        checked for the presence of missing data. These tests will pass if the
+        specified method of representing missing data was observed in the earlier
+        tests.
+
+        These tests check the capability to support the
+        [DataAbsentReason extension](http://hl7.org/fhir/R4/extension-data-absent-reason.html),
+        and the “unknown” concept code from the [DataAbsentReason Code System](http://terminology.hl7.org/CodeSystem/data-absent-reason).
+        It is intended to support manual verification (or other testing mechanism)
+        to fully test conformance to AU Core Missing Data and Suppressed Data requirements.
+      )
+      run_as_group
+
+      test do
+        id :au_core_missing_data
+        title 'Server represents missing data with the DataAbsentReason Extension and CodeSystem'
+        description %(
+          For non-coded data elements, servers SHALL use the DataAbsentReason
+          Extension to represent missing data in a required field.
+
+          For coded data elements with example, preferred, or extensible binding
+          strengths to ValueSets which do not include an appropriate "unknown"
+          code, servers SHALL use the "unknown" code from the DataAbsentReason
+          CodeSystem.
+        )
+
+        run do
+          profiles = RESOURCE_PROFILES.map { |profile| profile.split('/').last.gsub('-', '_').gsub('au_core_', '') }
+          profiles.each do |profile|
+            resource_type_key_string = "#{profile}_resources"
+            resources = scratch[resource_type_key_string.to_sym] || {}
+            all_resources = resources[:all] || []
+            all_resources = Helpers.return_uniq_list_resources(all_resources)
+            next unless all_resources.count.positive?
+
+            all_resources.each do |resource|
+              dar_codes_exists = Helpers.check_for_dar(resource)
+              dar_extension_exists = Helpers.check_for_dar_extension(resource)
+
+              info "Data Absent Reason code found for #{resource.resourceType} with id: #{resource.id}" if dar_codes_exists
+              info "Data Absent Reason extension found for #{resource.resourceType} with id: #{resource.id}" if dar_extension_exists
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/au_core_test_kit/custom_groups/smart_app_launch_group.rb

@@ -0,0 +1,167 @@
+# frozen_string_literal: true
+
+require 'smart_app_launch_test_kit'
+require_relative '../au_core_options'
+
+module AUCoreTestKit
+  class SmartAppLaunchGroup < Inferno::TestGroup
+    id :au_core_smart_app_launch
+    title 'SMART App Launch'
+
+    group do
+      required_suite_options AUCoreOptions::SMART_1_REQUIREMENT
+      id :au_core_smart_standalone_launch_stu1
+      title 'Standalone Launch'
+      optional
+
+      group from: :smart_discovery,
+            run_as_group: true
+      group from: :smart_standalone_launch,
+            run_as_group: true
+
+      group from: :smart_openid_connect do
+        run_as_group
+        optional
+        config(
+          inputs: {
+            id_token: { name: :standalone_id_token },
+            client_id: { name: :standalone_client_id },
+            requested_scopes: { name: :standalone_requested_scopes },
+            access_token: { name: :standalone_access_token },
+            smart_credentials: { name: :standalone_smart_credentials }
+          }
+        )
+      end
+
+      group from: :smart_token_refresh do
+        run_as_group
+        optional
+        config(
+          inputs: {
+            refresh_token: { name: :standalone_refresh_token },
+            client_id: { name: :standalone_client_id },
+            client_secret: { name: :standalone_client_secret },
+            received_scopes: { name: :standalone_received_scopes }
+          }
+        )
+      end
+    end
+
+    group do
+      required_suite_options AUCoreOptions::SMART_1_REQUIREMENT
+      id :au_core_smart_ehr_launch_stu1
+      title 'EHR Launch'
+      optional
+
+      group from: :smart_discovery,
+            run_as_group: true
+      group from: :smart_ehr_launch,
+            run_as_group: true
+
+      group from: :smart_openid_connect do
+        run_as_group
+        optional
+        config(
+          inputs: {
+            id_token: { name: :ehr_id_token },
+            client_id: { name: :ehr_client_id },
+            requested_scopes: { name: :ehr_requested_scopes },
+            access_token: { name: :ehr_access_token },
+            smart_credentials: { name: :ehr_smart_credentials }
+          }
+        )
+      end
+
+      group from: :smart_token_refresh do
+        run_as_group
+        optional
+        config(
+          inputs: {
+            refresh_token: { name: :ehr_refresh_token },
+            client_id: { name: :ehr_client_id },
+            client_secret: { name: :ehr_client_secret },
+            received_scopes: { name: :ehr_received_scopes }
+          }
+        )
+      end
+    end
+
+    group do
+      required_suite_options AUCoreOptions::SMART_2_REQUIREMENT
+      id :au_core_smart_standalone_launch_stu2
+      title 'Standalone Launch'
+      optional
+
+      group from: :smart_discovery_stu2,
+            run_as_group: true
+      group from: :smart_standalone_launch_stu2,
+            run_as_group: true
+
+      group from: :smart_openid_connect do
+        run_as_group
+        optional
+        config(
+          inputs: {
+            id_token: { name: :standalone_id_token },
+            client_id: { name: :standalone_client_id },
+            requested_scopes: { name: :standalone_requested_scopes },
+            access_token: { name: :standalone_access_token },
+            smart_credentials: { name: :standalone_smart_credentials }
+          }
+        )
+      end
+
+      group from: :smart_token_refresh do
+        run_as_group
+        optional
+        config(
+          inputs: {
+            refresh_token: { name: :standalone_refresh_token },
+            client_id: { name: :standalone_client_id },
+            client_secret: { name: :standalone_client_secret },
+            received_scopes: { name: :standalone_received_scopes }
+          }
+        )
+      end
+    end
+
+    group do
+      required_suite_options AUCoreOptions::SMART_2_REQUIREMENT
+      id :au_core_smart_ehr_launch_stu2
+      title 'EHR Launch'
+      optional
+
+      group from: :smart_discovery_stu2,
+            run_as_group: true
+      group from: :smart_ehr_launch_stu2,
+            run_as_group: true
+
+      group from: :smart_openid_connect do
+        run_as_group
+        optional
+        config(
+          inputs: {
+            id_token: { name: :ehr_id_token },
+            client_id: { name: :ehr_client_id },
+            requested_scopes: { name: :ehr_requested_scopes },
+            access_token: { name: :ehr_access_token },
+            smart_credentials: { name: :ehr_smart_credentials }
+          }
+        )
+      end
+
+      group from: :smart_token_refresh do
+        run_as_group
+        optional
+        config(
+          inputs: {
+            refresh_token: { name: :ehr_refresh_token },
+            client_id: { name: :ehr_client_id },
+            client_secret: { name: :ehr_client_secret },
+            received_scopes: { name: :ehr_received_scopes }
+          }
+        )
+      end
+    end
+  end
+end

data/lib/au_core_test_kit/custom_groups/v0.3.0-ballot/capability_statement_group.rb

@@ -0,0 +1,81 @@
+# frozen_string_literal: true
+
+require 'tls_test_kit'
+require_relative '../../helpers'
+require_relative '../capability_statement/conformance_support_test'
+require_relative '../capability_statement/fhir_version_test'
+require_relative '../capability_statement/json_support_test'
+require_relative '../capability_statement/xml_support_test'
+require_relative './profile_support_test'
+
+module AUCoreTestKit
+  module AUCoreV030_BALLOT
+    class CapabilityStatementGroup < Inferno::TestGroup
+      id :au_core_v030_ballot_capability_statement
+      title 'Capability Statement'
+      short_description 'Retrieve information about supported server functionality using the FHIR capabilties interaction.'
+      description Helpers.get_capability_statement_group_description_text('Capability Statement')
+      run_as_group
+
+      PROFILES = {
+        'AllergyIntolerance' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-allergyintolerance'],
+        'Condition' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-condition'],
+        'DiagnosticReport' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticreport'],
+        'DocumentReference' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-documentreference'],
+        'Encounter' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-encounter'],
+        'HealthcareService' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-healthcareservice'],
+        'Immunization' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-immunization'],
+        'Location' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-location'],
+        'Medication' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-medication'],
+        'MedicationRequest' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-medicationrequest'],
+        'MedicationStatement' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-medicationstatement'],
+        'Observation' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-bloodpressure',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-bmi',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-bodyheight',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-bodytemp',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-bodyweight',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult-imag',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult-path',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-lipid-result',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-headcircum',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-heartrate',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-observation',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-oxygensat',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-resprate',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-sexassignedatbirth',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-smokingstatus',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-vitalspanel',
+                          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-waistcircum'].freeze,
+        'Organization' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-organization'],
+        'Patient' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-patient'],
+        'Practitioner' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-practitioner'],
+        'PractitionerRole' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-practitionerrole'],
+        'Procedure' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-procedure'],
+        'Provenance' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-provenance'],
+        'ServiceRequest' => ['http://hl7.org.au/fhir/core/StructureDefinition/au-core-servicerequest']
+      }.freeze
+
+      test from: :tls_version_test,
+           id: :standalone_auth_tls,
+           title: 'FHIR server secured by transport layer security',
+           description: %(
+            Systems **SHALL** use TLS version 1.2 or higher for all transmissions
+            not taking place over a secure network connection.
+          ),
+           config: {
+             options: { minimum_allowed_version: OpenSSL::SSL::TLS1_2_VERSION }
+           }
+      test from: :au_core_conformance_support
+      test from: :au_core_fhir_version
+      test from: :au_core_json_support
+      test from: :au_core_xml_support
+
+      test from: :au_core_profile_support do
+        config(
+          options: { au_core_resources: PROFILES.keys }
+        )
+      end
+    end
+  end
+end

data/lib/au_core_test_kit/custom_groups/v0.3.0-ballot/profile_support_test.rb

@@ -0,0 +1,51 @@
+# frozen_string_literal: true
+
+module AUCoreTestKit
+  module AUCoreV030_BALLOT
+    class ProfileSupportTest < Inferno::Test
+      id :au_core_profile_support
+      title 'Capability Statement lists support for required AU Core Resoruce Types'
+      description %(
+        The AU Core Implementation Guide states:
+
+        ```
+        The AU Core Server SHALL:
+        1. Support the AU Core Patient resource.
+        2. Support at least one additional AU Core resources.
+        ```
+      )
+      uses_request :capability_statement
+
+      run do
+        assert_resource_type(:capability_statement)
+        capability_statement = resource
+
+        supported_resources =
+          capability_statement.rest
+                              &.each_with_object([]) do |rest, resources|
+            rest.resource.each { |resource| resources << resource.type }
+          end&.uniq
+
+        assert supported_resources.include?('Patient'), 'AU Core Patient profile not supported'
+
+        au_core_resources = config.options[:au_core_resources]
+
+        other_resources = au_core_resources.reject { |resource_type| resource_type == 'Patient' }
+        other_resources_supported = other_resources.any? { |resource| supported_resources.include? resource }
+        assert other_resources_supported, 'No AU Core resources other than Patient are supported'
+
+        if config.options[:required_resources].present?
+          missing_resources = config.options[:required_resources] - supported_resources
+
+          missing_resource_list =
+            missing_resources
+            .map { |resource| "`#{resource}`" }
+            .join(', ')
+
+          assert missing_resources.empty?,
+                 "The CapabilityStatement did not list support for the following resources: #{missing_resource_list}"
+        end
+      end
+    end
+  end
+end

data/lib/au_core_test_kit/custom_groups/v4.0.0/document_reference_custodian_test.rb

@@ -0,0 +1,50 @@
+# frozen_string_literal: true
+
+module AUCoreTestKit
+  module AUCoreV400
+    class DocumentReferenceCustodianTest < Inferno::Test
+      id :au_core_v400_document_reference_custodian_test
+      title 'DocumentReference resources returned during previous tests have custodian'
+      description %(
+        This test verifies the organization responsible for the DocumentReference is present either in DocumentReference.custodian
+        or accessible in the Provenance resource targeting the DocumentReference using Provenance.agent.who or Provenance.agent.onBehalfOf.
+      )
+
+      def scratch_resources
+        scratch[:document_reference_resources] ||= {}
+      end
+
+      def scratch_provenance_resources
+        scratch[:provenance_resources] ||= {}
+      end
+
+      run do
+        resources = scratch_resources[:all] || []
+        provenances = scratch_provenance_resources[:all] || []
+
+        skip_if resources.blank?,
+                'No DocumentReference resources appear to be available. ' \
+                'Please use patients with more information.'
+
+        resources.each do |docref|
+          has_custodian = docref.custodian.present?
+
+          if provenances.present?
+            has_agent = provenances.any? do |provenance|
+              provenance.target.any? { |target| target.reference.end_with?("DocumentReference/#{docref.id}") } &&
+                provenance.agent.any? { |agent| agent.who.present? || agent.onBehalfOf.present? }
+            end
+          end
+
+          unless has_custodian || has_agent
+            add_message('error',
+                        "DocumentReference/#{docref.id} does not have DocumentReference.custodian, Provenance.agent.who, nor Provenance.agent.onBehalfOf")
+          end
+        end
+
+        assert messages.blank?,
+               'Resource does not have DocumentReference.custodian, Provenance.agent.who, nor Provenance.agent.onBehalfOf'
+      end
+    end
+  end
+end

data/lib/au_core_test_kit/custom_suites/validation_suite.rb

@@ -0,0 +1,53 @@
+# frozen_string_literal: true
+
+require 'validation_test_kit/validation_test'
+
+module AUCoreTestKit
+  module AUCoreValidationSuite
+    class AUCoreTestSuite < Inferno::TestSuite
+      id :validations
+      title 'Validation Test Suite'
+      description 'Validation Test Suite'
+      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 AU Core v3.1.1
+        /Provenance.agent\[\d*\]: Rule provenance-1/, # Invalid invariant in AU Core v5.0.1
+        /\A\S+: \S+: URL value '.*' does not resolve/
+      ].freeze
+
+      VERSION_SPECIFIC_MESSAGE_FILTERS = [].freeze
+
+      def self.metadata
+        @metadata ||= YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true)[:groups].map do |raw_metadata|
+          Generator::GroupMetadata.new(raw_metadata)
+        end
+      end
+
+      fhir_resource_validator do
+        igs 'hl7.fhir.au.core#1.0.0-ballot'
+        message_filters = VALIDATION_MESSAGE_FILTERS + VERSION_SPECIFIC_MESSAGE_FILTERS
+
+        cli_context do
+          txServer ENV.fetch('TX_SERVER_URL', 'https://tx.dev.hl7.org.au/fhir')
+          disableDefaultResourceFetcher false
+        end
+
+        exclude_message do |message|
+          message_filters.any? { |filter| filter.match? message.message }
+        end
+      end
+
+      group do
+        title 'Validation of any FHIR resource'
+        test from: :validation_test,
+             config: {
+               options: {
+                 ig_version: '1.0.0-ballot'
+               }
+             }
+      end
+    end
+  end
+end