cancer_registry_reporting_test_kit 0.9.0

data/lib/cancer_registry_reporting_test_kit/hdea_generator/value_extractor.rb

@@ -0,0 +1,134 @@
+# frozen_string_literal: true
+
+module CancerRegistryReportingTestKit
+  class HdeaGenerator
+    class ValueExactor
+      attr_accessor :ig_resources, :resource, :profile_elements
+
+      def initialize(ig_resources, resource, profile_elements)
+        self.ig_resources = ig_resources
+        self.resource = resource
+        self.profile_elements = profile_elements
+      end
+
+      def values_from_fixed_codes(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        elements = profile_elements.select do |element|
+          element.path == "#{profile_element.path}.coding.code" && element.fixedCode.present?
+        end
+
+        elements.map(&:fixedCode)
+      end
+
+      def values_from_pattern_coding(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        elements = profile_elements.select do |element|
+          element.path == "#{profile_element.path}.coding" && element.patternCoding.present?
+        end
+
+        elements.map { |element| element.patternCoding.code }
+      end
+
+      def values_from_pattern_codeable_concept(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        elements = profile_elements.select do |element|
+          element.path == profile_element.path && element.patternCodeableConcept.present? && element.min.positive?
+        end
+
+        elements.map { |element| element.patternCodeableConcept.coding.first.code }
+      end
+
+      def value_set_binding(the_element)
+        the_element&.binding
+      end
+
+      def value_set(the_element)
+        ig_resources.value_set_by_url(value_set_binding(the_element)&.valueSet)
+      end
+
+      def bound_systems(the_element)
+        bound_systems_from_valueset(value_set(the_element))
+      end
+
+      def bound_systems_from_valueset(value_set)
+        value_set&.compose&.include&.map do |include_element|
+          if include_element.concept.present?
+            include_element
+          elsif include_element.system.present? && include_element.filter&.empty?
+            # Cannot process intensional value set with filters
+            ig_resources.code_system_by_url(include_element.system)
+          elsif include_element.valueSet.present?
+            include_element.valueSet.map do |vs|
+              a_value_set = ig_resources.value_set_by_url(vs)
+              bound_systems_from_valueset(a_value_set)
+            end
+          end
+        end&.flatten&.compact
+      end
+
+      def codes_from_value_set_binding(the_element)
+        codes_from_system_code_pair(codings_from_value_set_binding(the_element))
+      end
+
+      def codes_from_system_code_pair(codings)
+        codings.present? ? codings.map { |coding| coding[:code] }.compact.uniq : []
+      end
+
+      def codings_from_value_set_binding(the_element)
+        return [] if the_element.nil?
+
+        bound_systems = bound_systems(the_element)
+
+        return codings_from_bound_systems(bound_systems) if bound_systems.present?
+
+        expansion_contains = value_set_expansion_contains(the_element)
+
+        return [] if expansion_contains.blank?
+
+        expansion_contains.map { |contains| { system: contains.system, code: contains.code } }.compact.uniq
+      end
+
+      def codings_from_bound_systems(bound_systems)
+        return [] unless bound_systems.present?
+
+        bound_systems.flat_map do |bound_system|
+          case bound_system
+          when FHIR::ValueSet::Compose::Include
+            bound_system.concept.map { |concept| { system: bound_system.system, code: concept.code } }
+          when FHIR::CodeSystem
+            bound_system.concept.map { |concept| { system: bound_system.url, code: concept.code } }
+          else
+            []
+          end
+        end.uniq
+      end
+
+      def value_set_expansion_contains(element)
+        value_set(element)&.expansion&.contains
+      end
+
+      def fhir_metadata(current_path)
+        FHIR.const_get(resource)::METADATA[current_path]
+      end
+
+      def values_from_resource_metadata(paths)
+        values = []
+
+        paths.each do |current_path|
+          current_metadata = fhir_metadata(current_path)
+
+          next unless current_metadata&.dig('valid_codes').present?
+
+          values += current_metadata['valid_codes'].flat_map do |system, codes|
+            codes.map { |code| { system:, code: } }
+          end
+        end
+
+        values
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_generator.rb

@@ -0,0 +1,66 @@
+# frozen_string_literal: true
+
+require 'fhir_models'
+require 'inferno/ext/fhir_models'
+
+require_relative 'hdea_generator/ig_loader'
+require_relative 'hdea_generator/ig_metadata_extractor'
+require_relative 'hdea_generator/group_generator'
+require_relative 'hdea_generator/must_support_test_generator'
+require_relative 'hdea_generator/validation_test_generator'
+require_relative 'hdea_generator/special_cases'
+
+module CancerRegistryReportingTestKit
+  class HdeaGenerator
+    def self.generate
+      ig_packages = Dir.glob(File.join(Dir.pwd, 'lib', 'cancer_registry_reporting_test_kit', 'igs', '*.tgz'))
+
+      ig_packages.each do |ig_package|
+        new(ig_package).generate
+      end
+    end
+
+    attr_accessor :ig_resources, :ig_metadata, :ig_file_name
+
+    def initialize(ig_file_name)
+      self.ig_file_name = ig_file_name
+    end
+
+    def generate
+      puts "Generating tests for IG #{File.basename(ig_file_name)}"
+      load_ig_package
+      extract_metadata
+      generate_must_support_tests
+      generate_validation_tests
+      generate_groups
+    end
+
+    def extract_metadata
+      self.ig_metadata = IGMetadataExtractor.new(ig_resources).extract
+
+      FileUtils.mkdir_p(base_output_dir)
+    end
+
+    def base_output_dir
+      File.join(__dir__, 'hdea_suite', 'generated', ig_metadata.ig_version)
+    end
+
+    def load_ig_package
+      FHIR.logger = Logger.new(File::NULL)
+      self.ig_resources = IGLoader.new(ig_file_name).load
+    end
+
+    def generate_validation_tests
+      ValidationTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_must_support_tests
+      MustSupportTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_groups
+      # SpecialCases.move_ms_and_validation(ig_metadata)
+      GroupGenerator.generate(ig_metadata, base_output_dir)
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/author/author_validation_test.rb

@@ -0,0 +1,61 @@
+# frozen_string_literal: true
+
+require_relative '../../validation_test'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class AuthorValidationTest < Inferno::Test
+      include CancerRegistryReportingTestKit::ValidationTest
+
+      id :ccrr_v100_author_validation_test
+      title 'Author resources returned during previous tests conform to the US Core Practitioner Role, Practitioner, or Organization Profile'
+      description %(
+This test verifies that author resources referenced in the provided cancer report conform to
+the [US Core PractitionerRole Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole),
+[US Core Practitioner Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner), or
+[US Core Organization Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization).
+Systems must demonstrate at least one valid example in order to pass this test.
+
+It verifies the presence of mandatory elements and that elements with
+required bindings contain appropriate values. CodeableConcept element
+bindings will fail if none of their codings have a code/system belonging
+to the bound ValueSet. Quantity, Coding, and code element bindings will
+fail if their code/system are not found in the valueset.
+
+      )
+
+      def scratch_resources
+        scratch[:author_resources] ||= {}
+      end
+
+      AUTHOR_PROFILES = {
+        'PractitionerRole' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole',
+        'Practitioner' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner',
+        'Organization' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization'
+      }.freeze
+
+      run do
+        resources_by_type = {
+          'PractitionerRole' => [],
+          'Practitioner' => [],
+          'Organization' => []
+        }
+
+        scratch_resources[:all]&.each do |author|
+          resources_by_type[author.resourceType] << author
+        end
+
+        resources_by_type.each do |resource_type, resources|
+          next if resources.blank?
+
+          perform_validation_test(
+            resource_type,
+            resources,
+            AUTHOR_PROFILES[resource_type],
+            '3.1.1'
+          )
+        end
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/author/organization_metadata.yml

@@ -0,0 +1,47 @@
+---
+:name: us_core_organization
+:class_name: UsCoreOrganizationSequence
+:version: v1.0.0
+:reformatted_version: v100
+:resource: Organization
+:profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization
+:profile_name: US Core Organization Profile
+:profile_version: 5.0.1
+:title: US Core Organization
+:short_description: Verify support for the server capabilities required by the US
+  Core Organization Profile.
+:must_supports:
+  :extensions: []
+  :slices:
+  - :slice_id: Organization.identifier:NPI
+    :slice_name: NPI
+    :path: identifier
+    :discriminator:
+      :type: patternIdentifier
+      :path: ''
+      :system: http://hl7.org/fhir/sid/us-npi
+  :elements:
+  - :path: identifier
+  - :path: identifier.system
+  - :path: identifier.value
+  - :path: active
+  - :path: name
+  - :path: telecom
+  - :path: telecom.system
+  - :path: telecom.value
+  - :path: address
+  - :path: address.line
+  - :path: address.city
+  - :path: address.state
+  - :path: address.postalCode
+  - :path: address.country
+:mandatory_elements:
+- Organization.active
+- Organization.name
+:tests:
+- :id: ccrr_v100_organization_must_support_test
+  :file_name: organization_must_support_test.rb
+- :id: ccrr_v100_organization_validation_test
+  :file_name: organization_validation_test.rb
+:id: ccrr_v100_organization
+:file_name: organization_group.rb

data/lib/cancer_registry_reporting_test_kit/hdea_suite/author/organization_must_support_test.rb

@@ -0,0 +1,73 @@
+# frozen_string_literal: true
+
+require_relative '../../must_support_test'
+require_relative '../../hdea_generator/group_metadata'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class OrganizationMustSupportTest < Inferno::Test
+      include CancerRegistryReportingTestKit::MustSupportTest
+
+      title 'All must support elements are provided in the Organization resources returned'
+      description %(
+        US Core Responders SHALL be capable of populating all data elements as
+        part of the query results as specified by the US Core Server Capability
+        Statement. This test will look through the Organization resources
+        found previously for the following must support elements:
+
+        * Organization.active
+        * Organization.address
+        * Organization.address.city
+        * Organization.address.country
+        * Organization.address.line
+        * Organization.address.postalCode
+        * Organization.address.state
+        * Organization.identifier
+        * Organization.identifier.system
+        * Organization.identifier.value
+        * Organization.identifier:NPI
+        * Organization.name
+        * Organization.telecom
+        * Organization.telecom.system
+        * Organization.telecom.value
+      )
+
+      id :ccrr_v100_organization_must_support_test
+
+      def resource_type
+        'Organization'
+      end
+
+      def self.metadata
+        @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'organization_metadata.yml'),
+                                                                      aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:author_resources] ||= {}
+      end
+
+      AUTHOR_PROFILES = {
+        'PractitionerRole' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole',
+        'Practitioner' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner',
+        'Organization' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization'
+      }.freeze
+
+      run do
+        resources_by_type = {
+          'PractitionerRole' => [],
+          'Practitioner' => [],
+          'Organization' => []
+        }
+
+        scratch_resources[:all]&.each do |author|
+          resources_by_type[author.resourceType] << author
+        end
+
+        skip if resources_by_type['Practitioner'].empty? && resources_by_type['PractitionerRole'].empty? && resources_by_type['Organization'].empty?
+        omit if resources_by_type['Organization'].empty?
+        perform_must_support_test(resources_by_type['Organization'])
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/author/practitioner_metadata.yml

@@ -0,0 +1,51 @@
+---
+:name: us_core_practitioner
+:class_name: UsCorePractitionerSequence
+:version: v1.0.0
+:reformatted_version: v100
+:resource: Practitioner
+:profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner
+:profile_name: US Core Practitioner Profile
+:profile_version: 5.0.1
+:title: US Core Practitioner
+:short_description: Verify support for the server capabilities required by the US
+  Core Practitioner Profile.
+:must_supports:
+  :extensions: []
+  :slices:
+  - :slice_id: Practitioner.identifier:NPI
+    :slice_name: NPI
+    :path: identifier
+    :discriminator:
+      :type: patternIdentifier
+      :path: ''
+      :system: http://hl7.org/fhir/sid/us-npi
+  :elements:
+  - :path: identifier
+  - :path: identifier.system
+  - :path: identifier.value
+  - :path: name
+  - :path: name.family
+  - :path: telecom
+  - :path: telecom.system
+  - :path: telecom.value
+  - :path: address
+  - :path: address.line
+  - :path: address.city
+  - :path: address.state
+  - :path: address.postalCode
+  - :path: address.country
+:mandatory_elements:
+- Practitioner.identifier
+- Practitioner.identifier.system
+- Practitioner.identifier.value
+- Practitioner.name
+- Practitioner.name.family
+- Practitioner.qualification.code
+:tests:
+- :id: ccrr_v100_practitioner_must_support_test
+  :file_name: practitioner_must_support_test.rb
+- :id: ccrr_v100_practitioner_validation_test
+  :file_name: practitioner_validation_test.rb
+:id: ccrr_v100_practitioner
+:file_name: practitioner_group.rb

data/lib/cancer_registry_reporting_test_kit/hdea_suite/author/practitioner_must_support_test.rb

@@ -0,0 +1,73 @@
+# frozen_string_literal: true
+
+require_relative '../../must_support_test'
+require_relative '../../hdea_generator/group_metadata'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class PractitionerMustSupportTest < Inferno::Test
+      include CancerRegistryReportingTestKit::MustSupportTest
+
+      title 'All must support elements are provided in the Practitioner resources returned'
+      description %(
+        US Core Responders SHALL be capable of populating all data elements as
+        part of the query results as specified by the US Core Server Capability
+        Statement. This test will look through the Practitioner resources
+        found previously for the following must support elements:
+
+        * Practitioner.address
+        * Practitioner.address.city
+        * Practitioner.address.country
+        * Practitioner.address.line
+        * Practitioner.address.postalCode
+        * Practitioner.address.state
+        * Practitioner.identifier
+        * Practitioner.identifier.system
+        * Practitioner.identifier.value
+        * Practitioner.identifier:NPI
+        * Practitioner.name
+        * Practitioner.name.family
+        * Practitioner.telecom
+        * Practitioner.telecom.system
+        * Practitioner.telecom.value
+      )
+
+      id :ccrr_v100_practitioner_must_support_test
+
+      def resource_type
+        'Practitioner'
+      end
+
+      def self.metadata
+        @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'practitioner_metadata.yml'),
+                                                                      aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:author_resources] ||= {}
+      end
+
+      AUTHOR_PROFILES = {
+        'PractitionerRole' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole',
+        'Practitioner' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner',
+        'Organization' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization'
+      }.freeze
+
+      run do
+        resources_by_type = {
+          'PractitionerRole' => [],
+          'Practitioner' => [],
+          'Organization' => []
+        }
+
+        scratch_resources[:all]&.each do |author|
+          resources_by_type[author.resourceType] << author
+        end
+
+        skip if resources_by_type['Practitioner'].empty? && resources_by_type['PractitionerRole'].empty? && resources_by_type['Organization'].empty?
+        omit if resources_by_type['Practitioner'].empty?
+        perform_must_support_test(resources_by_type['Practitioner'])
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/author/practitioner_role_metadata.yml

@@ -0,0 +1,48 @@
+---
+:name: us_core_practitionerrole
+:class_name: UsCorePractitionerroleSequence
+:version: v1.0.0
+:reformatted_version: v100
+:resource: PractitionerRole
+:profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole
+:profile_name: US Core PractitionerRole Profile
+:profile_version: 5.0.1
+:title: US Core PractitionerRole
+:short_description: Verify support for the server capabilities required by the US
+  Core PractitionerRole Profile.
+:must_supports:
+  :extensions: []
+  :slices: []
+  :elements:
+  - :path: practitioner
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner
+  - :path: organization
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization
+  - :path: code
+  - :path: specialty
+  - :path: location
+    :types:
+    - Reference
+  - :path: telecom
+  - :path: telecom.system
+  - :path: telecom.value
+  - :path: endpoint
+    :types:
+    - Reference
+:mandatory_elements:
+- PractitionerRole.telecom.system
+- PractitionerRole.telecom.value
+- PractitionerRole.notAvailable.description
+:tests:
+- :id: ccrr_v100_practitioner_role_must_support_test
+  :file_name: practitioner_role_must_support_test.rb
+- :id: ccrr_v100_practitioner_role_validation_test
+  :file_name: practitioner_role_validation_test.rb
+:id: ccrr_v100_practitioner_role
+:file_name: practitioner_role_group.rb

data/lib/cancer_registry_reporting_test_kit/hdea_suite/author/practitioner_role_must_support_test.rb

@@ -0,0 +1,66 @@
+# frozen_string_literal: true
+
+require_relative '../../must_support_test'
+require_relative '../../hdea_generator/group_metadata'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class PractitionerRoleMustSupportTest < Inferno::Test
+      include CancerRegistryReportingTestKit::MustSupportTest
+
+      title 'All must support elements are provided in the Practitioner Role resources returned'
+      description %(
+        US Core Responders SHALL be capable of populating all data elements as
+        part of the query results as specified by the US Core Server Capability
+        Statement. This test will look through the PractitionerRole resources
+        found previously for the following must support elements:
+
+        * PractitionerRole.code
+        * PractitionerRole.endpoint
+        * PractitionerRole.location
+        * PractitionerRole.organization
+        * PractitionerRole.practitioner
+        * PractitionerRole.specialty
+        * PractitionerRole.telecom
+        * PractitionerRole.telecom.system
+        * PractitionerRole.telecom.value
+      )
+
+      id :ccrr_v100_practitioner_role_must_support_test
+
+      def resource_type
+        'PractitionerRole'
+      end
+
+      def self.metadata
+        @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:author_resources] ||= {}
+      end
+
+      AUTHOR_PROFILES = {
+        'PractitionerRole' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole',
+        'Practitioner' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner',
+        'Organization' => 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization'
+      }.freeze
+
+      run do
+        resources_by_type = {
+          'PractitionerRole' => [],
+          'Practitioner' => [],
+          'Organization' => []
+        }
+
+        scratch_resources[:all]&.each do |author|
+          resources_by_type[author.resourceType] << author
+        end
+
+        skip if resources_by_type['Practitioner'].empty? && resources_by_type['PractitionerRole'].empty? && resources_by_type['Organization'].empty?
+        omit if resources_by_type['PractitionerRole'].empty?
+        perform_must_support_test(resources_by_type['PractitionerRole'])
+      end
+    end
+  end
+end