cancer_registry_reporting_test_kit 0.9.0

data/lib/cancer_registry_reporting_test_kit/hdea_generator/ig_loader.rb

@@ -0,0 +1,78 @@
+# frozen_string_literal: true
+
+require 'active_support/all'
+require 'fhir_models'
+require 'pathname'
+require 'rubygems/package'
+require 'zlib'
+require_relative 'ig_resources'
+
+module CancerRegistryReportingTestKit
+  class HdeaGenerator
+    class IGLoader
+      attr_accessor :ig_file_name
+
+      def initialize(ig_file_name)
+        self.ig_file_name = ig_file_name
+      end
+
+      def ig_resources
+        @ig_resources ||= IGResources.new
+      end
+
+      def load
+        load_ig
+        load_standalone_resources
+      end
+
+      def load_ig
+        tar = Gem::Package::TarReader.new(
+          Zlib::GzipReader.open(ig_file_name)
+        )
+
+        tar.each do |entry|
+          next if entry.directory?
+
+          file_name = entry.full_name.split('/').last
+
+          next if file_name.end_with? 'package.json'
+
+          next unless file_name.end_with? '.json'
+          next unless entry.full_name.start_with? 'package/'
+
+          begin
+            resource = FHIR.from_contents(entry.read)
+            next if resource.nil?
+          rescue StandardError
+            puts "#{file_name} does not appear to be a FHIR resource."
+            next
+          end
+
+          ig_resources.add(resource)
+        end
+
+        ig_resources
+      end
+
+      def load_standalone_resources
+        ig_directory = ig_file_name.chomp('.tgz')
+
+        return ig_resources unless File.exist? ig_directory
+
+        Dir.glob(File.join(ig_directory, '*.json')).each do |file_path|
+          begin
+            resource = FHIR.from_contents(File.read(file_path))
+            next if resource.nil?
+          rescue StandardError
+            file_name = file_path.split('/').last
+            puts "#{file_name} does not appear to be a FHIR resource (standalone)."
+            next
+          end
+          ig_resources.add(resource)
+        end
+
+        ig_resources
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_generator/ig_metadata.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require_relative 'special_cases'
+require 'pry'
+module CancerRegistryReportingTestKit
+  class HdeaGenerator
+    class IGMetadata
+      attr_accessor :ig_version, :groups
+
+      def reformatted_version
+        @reformatted_version ||= ig_version.delete('.').gsub('-', '_')
+      end
+
+      def ordered_groups
+        @ordered_groups ||= groups
+      end
+
+      def to_hash
+        {
+          ig_version: ig_version,
+          groups: groups.map(&:to_hash)
+        }
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_generator/ig_metadata_extractor.rb

@@ -0,0 +1,78 @@
+# frozen_string_literal: true
+
+require_relative 'ig_metadata'
+require_relative 'group_metadata_extractor'
+
+module CancerRegistryReportingTestKit
+  class HdeaGenerator
+    class IGMetadataExtractor
+      attr_accessor :ig_resources, :metadata
+
+      def initialize(ig_resources)
+        self.ig_resources = ig_resources
+        add_missing_supported_profiles
+        remove_version_from_supported_profiles
+        self.metadata = IGMetadata.new
+      end
+
+      def extract
+        add_metadata_from_ig
+        add_metadata_from_resources
+        metadata
+      end
+
+      def add_metadata_from_ig
+        metadata.ig_version = "v#{ig_resources.ig.version}"
+      end
+
+      def resources_in_capability_statement
+        ig_resources.capability_statement.rest.first.resource
+      end
+
+      def resources_in_structure_definitions
+        ig_resources.resources_by_type['StructureDefinition'].map
+      end
+
+      def add_missing_supported_profiles
+        case ig_resources.ig.version
+        when '3.1.1'
+          # The US Core v3.1.1 Server Capability Statement does not list support for the
+          # required vital signs profiles, so they need to be added
+          ig_resources.capability_statement.rest.first.resource
+            .find { |resource| resource.type == 'Observation' }
+            .supportedProfile.concat [ 
+                        'http://hl7.org/fhir/StructureDefinition/bodyheight',
+                        'http://hl7.org/fhir/StructureDefinition/bodytemp',
+                        'http://hl7.org/fhir/StructureDefinition/bp',
+                        'http://hl7.org/fhir/StructureDefinition/bodyweight',
+                        'http://hl7.org/fhir/StructureDefinition/heartrate',
+                        'http://hl7.org/fhir/StructureDefinition/resprate'
+            ]
+                      
+        when '5.0.1'
+          # The US Core v5.0.1 Server Capability Statement does not have supported-profile for Encounter
+          ig_resources.capability_statement.rest.first.resource
+            .find { |resource| resource.type == 'Encounter' }
+            .supportedProfile.concat [
+                        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter'
+            ]
+                      
+        end
+      end
+
+      def remove_version_from_supported_profiles
+        resources_in_capability_statement.each do |resource|
+          resource.supportedProfile.map! { |profile_url| profile_url.split('|').first }
+        end
+      end
+
+      def add_metadata_from_resources
+        metadata.groups =
+          resources_in_structure_definitions.flat_map do |resource|
+            supported_profile = resource.url
+            GroupMetadataExtractor.new(resource, supported_profile, metadata, ig_resources).group_metadata
+          end.compact
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_generator/ig_resources.rb

@@ -0,0 +1,56 @@
+# frozen_string_literal: true
+
+module CancerRegistryReportingTestKit
+  class HdeaGenerator
+    class IGResources
+      def add(resource)
+        resources_by_type[resource.resourceType] << resource
+      end
+
+      def capability_statement(mode = 'server')
+        resources_by_type['CapabilityStatement'].find do |capability_statement_resource|
+          capability_statement_resource.rest.any? { |r| r.mode == mode }
+        end
+      end
+
+      def ig
+        resources_by_type['ImplementationGuide'].first
+      end
+
+      def inspect
+        'IGResources'
+      end
+
+      def profile_by_url(url)
+        resources_by_type['StructureDefinition'].find { |profile| profile.url == url }
+      end
+
+      def resource_for_profile(url)
+        resources_by_type['StructureDefinition'].find { |profile| profile.url == url }.type
+      end
+
+      def value_set_by_url(url)
+        resources_by_type['ValueSet'].find { |profile| profile.url == url }
+      end
+
+      def code_system_by_url(url)
+        resources_by_type['CodeSystem'].find { |system| system.url == url }
+      end
+
+      def search_param_by_resource_and_name(resource, name)
+        # remove '_' from search parameter name, such as _id or _tag
+        normalized_name = name.to_s.delete_prefix('_')
+
+        resources_by_type['SearchParameter'].find do |param|
+          param.id == "us-core-#{resource.downcase}-#{normalized_name}" || param.name == name
+        end
+      end
+
+      # private
+
+      def resources_by_type
+        @resources_by_type ||= Hash.new { |hash, key| hash[key] = [] }
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_generator/must_support_metadata_extractor.rb

@@ -0,0 +1,399 @@
+# frozen_string_literal: true
+
+require_relative 'value_extractor'
+
+module CancerRegistryReportingTestKit
+  class HdeaGenerator
+    class MustSupportMetadataExtractor
+      attr_accessor :profile_elements, :profile, :resource, :ig_resources
+
+      def initialize(profile_elements, profile, resource, ig_resources)
+        self.profile_elements = profile_elements
+        self.profile = profile
+        self.resource = resource
+        self.ig_resources = ig_resources
+      end
+
+      def must_supports
+        @must_supports = {
+          extensions: must_support_extensions,
+          slices: must_support_slices,
+          elements: must_support_elements
+        }
+
+        @must_supports
+      end
+
+      def is_uscdi_requirement_element?(element)
+        element.extension.any? do |extension|
+          extension.url == 'http://hl7.org/fhir/us/core/StructureDefinition/uscdi-requirement' &&
+            extension.valueBoolean
+        end && !element.mustSupport
+      end
+
+      def all_must_support_elements
+        profile_elements.select do |element| 
+          element.path != resource && (element.mustSupport || is_uscdi_requirement_element?(element))
+        end
+      end
+
+      def must_support_extension_elements
+        all_must_support_elements.select { |element| element.path.end_with? 'extension' }
+      end
+
+      def must_support_extensions
+        must_support_extension_elements.map do |element|
+          next unless element.type.first.profile.present?
+          {
+            id: element.id,
+            path: element.path.gsub("#{resource}.", ''),
+            url: element.type.first.profile.first
+          }.tap do |metadata|
+            metadata[:uscdi_only] = true if is_uscdi_requirement_element?(element)
+          end
+        end.compact
+      end
+
+      def must_support_slice_elements
+        all_must_support_elements.select do |element|
+          !element.path.end_with?('extension') && element.sliceName.present?
+        end
+      end
+
+      def sliced_element(slice)
+        profile_elements.find do |element|
+          element.id == slice.path || element.id == slice.id.sub(":#{slice.sliceName}", '')
+        end
+      end
+
+      def discriminators(slice)
+        slice&.slicing&.discriminator
+      end
+
+      def must_support_pattern_slice_elements
+        must_support_slice_elements.select do |element|
+          discriminators(sliced_element(element))&.first&.type == 'pattern'
+        end
+      end
+
+      def pattern_slices
+        must_support_pattern_slice_elements.map do |current_element|
+          {
+            slice_id: current_element.id,
+            slice_name: current_element.sliceName,
+            path: current_element.path.gsub("#{resource}.", '')
+          }.tap do |metadata|
+            discriminator = discriminators(sliced_element(current_element)).first
+            discriminator_path = discriminator.path
+            discriminator_path = '' if discriminator_path == '$this'
+            pattern_element =
+              if discriminator_path.present?
+                profile_elements.find { |element| element.id == "#{current_element.id}.#{discriminator_path}" }
+              else
+                current_element
+              end
+            metadata[:discriminator] =
+              if pattern_element.patternCodeableConcept.present?
+                {
+                  type: 'patternCodeableConcept',
+                  path: discriminator_path,
+                  code: pattern_element.patternCodeableConcept.coding.first.code,
+                  system: pattern_element.patternCodeableConcept.coding.first.system
+                }
+              elsif pattern_element.patternCoding.present?
+                {
+                  type: 'patternCoding',
+                  path: discriminator_path,
+                  code: pattern_element.patternCoding.code,
+                  system: pattern_element.patternCoding.system
+                }
+              elsif pattern_element.patternIdentifier.present?
+                {
+                  type: 'patternIdentifier',
+                  path: discriminator_path,
+                  system: pattern_element.patternIdentifier.system
+                }
+              elsif pattern_element.binding&.strength == 'required' &&
+                    pattern_element.binding&.valueSet.present?
+
+                value_extractor = ValueExactor.new(ig_resources, resource, profile_elements)
+
+                values = value_extractor.codings_from_value_set_binding(pattern_element).presence ||
+                         value_extractor.values_from_resource_metadata([metadata[:path]]).presence || []
+
+                {
+                  type: 'requiredBinding',
+                  path: discriminator_path,
+                  values: values
+                }
+              else
+                raise StandardError, 'Unsupported discriminator pattern type'
+              end
+
+            metadata[:uscdi_only] = true if is_uscdi_requirement_element?(current_element)
+          end
+        end
+      end
+
+      def must_support_type_slice_elements
+        must_support_slice_elements.select do |element|
+          discriminators(sliced_element(element))&.first&.type == 'type'
+        end
+      end
+
+      def type_slices
+        must_support_type_slice_elements.map do |current_element|
+          discriminator = discriminators(sliced_element(current_element)).first
+          type_path = discriminator.path
+          type_path = '' if type_path == '$this'
+          type_element =
+            if type_path.present?
+              profile_elements.find { |element| element.id == "#{current_element.id}.#{type_path}" }
+            else
+              current_element
+            end
+
+          type_code = type_element.type.first.code
+
+          {
+            slice_id: current_element.id,
+            slice_name: current_element.sliceName,
+            path: current_element.path.gsub("#{resource}.", ''),
+            discriminator: {
+              type: 'type',
+              code: type_code.upcase_first
+            }
+          }.tap do |metadata|
+            metadata[:uscdi_only] = true if is_uscdi_requirement_element?(current_element)
+          end
+        end
+      end
+
+      def must_support_value_slice_elements
+        must_support_slice_elements.select do |element|
+          discriminators(sliced_element(element))&.first&.type == 'value'
+        end
+      end
+
+      def value_slices
+        must_support_value_slice_elements.map do |current_element|
+          {
+            slice_id: current_element.id,
+            slice_name: current_element.sliceName,
+            path: current_element.path.gsub("#{resource}.", ''),
+            discriminator: {
+              type: 'value'
+            }
+          }.tap do |metadata|
+            metadata[:discriminator][:values] = discriminators(sliced_element(current_element)).map do |discriminator|
+              fixed_element = profile_elements.find do |element|
+                element.id.starts_with?(current_element.id) &&
+                  element.path == "#{current_element.path}.#{discriminator.path}"
+              end
+
+              if fixed_element.patternCodeableConcept.present?
+                code_value = fixed_element.patternCodeableConcept.coding.first.code
+                {
+                  path: "#{discriminator.path}.coding.code",
+                  value: code_value !~ /\D/ ? code_value.to_i : code_value
+                }
+              else
+                {
+                  path: discriminator.path,
+                  value: fixed_element.fixedUri || fixed_element.fixedCode
+                }
+              end
+              
+            end
+
+            metadata[:uscdi_only] = true if is_uscdi_requirement_element?(current_element)
+          end
+        end
+      end
+
+      def must_support_slices
+        pattern_slices + type_slices + value_slices
+      end
+
+      def plain_must_support_elements
+        all_must_support_elements - must_support_extension_elements - must_support_slice_elements
+      end
+
+      def element_part_of_slice_discrimination?(element)
+        must_support_slice_elements.any? { |ms_slice| element.id.include?(ms_slice.id) }
+      end
+
+      def handle_fixed_values(metadata, element)
+        if element.fixedUri.present?
+          metadata[:fixed_value] = element.fixedUri
+        elsif element.patternCodeableConcept.present? && !element_part_of_slice_discrimination?(element)
+          metadata[:fixed_value] = element.patternCodeableConcept.coding.first.code
+          metadata[:path] += '.coding.code'
+        elsif element.fixedCode.present?
+          metadata[:fixed_value] = element.fixedCode
+        elsif element.patternIdentifier.present? && !element_part_of_slice_discrimination?(element)
+          metadata[:fixed_value] = element.patternIdentifier.system
+          metadata[:path] += '.system'
+        end
+      end
+
+      def type_must_support_extension?(extensions)
+        extensions&.any? do |extension|
+          extension.url == 'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support' &&
+            extension.valueBoolean
+        end
+      end
+
+      def save_type_code?(type)
+        type.code == 'Reference'
+      end
+
+      def get_type_must_support_metadata(current_metadata, current_element)
+        current_element.type.map do |type|
+          next unless type_must_support_extension?(type.extension)
+
+          metadata =
+            {
+              path: "#{current_metadata[:path].delete_suffix('[x]')}#{type.code.upcase_first}",
+              original_path: current_metadata[:path]
+            }
+          metadata[:types] = [type.code] if save_type_code?(type)
+          handle_type_must_support_target_profiles(type, metadata) if type.code == 'Reference'
+
+          metadata
+        end.compact
+      end
+
+      def handle_type_must_support_target_profiles(type, metadata)
+        # US Core 3.1.1 profiles do not have US Core target profiles.
+        # Vital Sign proifles from FHIR R4 (version 4.0.1) do not have US Core target profiles either.
+        return if ['3.1.1', '4.0.1'].include?(profile.version)
+
+        target_profiles = []
+
+        if type.targetProfile&.length == 1
+          target_profiles << type.targetProfile.first
+        else
+          type.source_hash['_targetProfile']&.each_with_index do |hash, index|
+            if hash.present?
+              element = FHIR::Element.new(hash)
+              target_profiles << type.targetProfile[index] if type_must_support_extension?(element.extension)
+            end
+          end
+        end
+
+        # remove target_profile for FHIR Base resource type.
+        target_profiles.delete_if { |reference| reference.start_with?('http://hl7.org/fhir/StructureDefinition') }
+        metadata[:target_profiles] = target_profiles if target_profiles.present?
+      end
+
+      def handle_choice_type_in_sliced_element(current_metadata, must_support_elements_metadata)
+        choice_element_metadata = must_support_elements_metadata.find do |metadata|
+          metadata[:original_path].present? &&
+            current_metadata[:path].include?(metadata[:original_path])
+        end
+
+        return unless choice_element_metadata.present?
+
+        current_metadata[:original_path] = current_metadata[:path]
+        current_metadata[:path] =
+          current_metadata[:path].sub(choice_element_metadata[:original_path], choice_element_metadata[:path])
+      end
+
+      def must_support_elements
+        plain_must_support_elements.each_with_object([]) do |current_element, must_support_elements_metadata|
+          {
+            path: current_element.id.gsub("#{resource}.", '')
+          }.tap do |current_metadata|
+            current_metadata[:uscdi_only] = true if is_uscdi_requirement_element?(current_element)
+
+            type_must_support_metadata = get_type_must_support_metadata(current_metadata, current_element)
+
+            if type_must_support_metadata.any?
+              must_support_elements_metadata.concat(type_must_support_metadata)
+            else
+              handle_choice_type_in_sliced_element(current_metadata, must_support_elements_metadata)
+
+              supported_types = current_element.type.select { |type| save_type_code?(type) }.map(&:code)
+              current_metadata[:types] = supported_types if supported_types.present?
+
+              if current_element.type.first&.code == 'Reference'
+                handle_type_must_support_target_profiles(current_element.type.first,
+                                                         current_metadata)
+              end
+
+              handle_fixed_values(current_metadata, current_element)
+
+              must_support_elements_metadata.delete_if do |metadata|
+                metadata[:path] == current_metadata[:path] && metadata[:fixed_value].blank?
+              end
+
+              must_support_elements_metadata << current_metadata
+            end
+          end
+        end.uniq
+      end
+
+      #### SPECIAL CASE ####
+
+      def is_vital_sign?
+        [
+          'http://hl7.org/fhir/StructureDefinition/vitalsigns',
+          'http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs'
+        ].include?(profile.baseDefinition)
+      end
+
+      def is_blood_pressure?
+        %w[bp us-core-blood-pressure us-core-average-blood-pressure].include?(profile.id)
+      end
+
+      # Exclude Observation.component from vital sign profiles except observation-bp and observation-pulse-ox
+      def remove_vital_sign_component
+        return if is_blood_pressure? || profile.name == 'USCorePulseOximetryProfile'
+
+        return unless is_vital_sign?
+
+        @must_supports[:elements].delete_if do |element|
+          element[:path].start_with?('component')
+        end
+      end
+
+      # Exclude Observation.value[x] from observation-bp
+      def remove_blood_pressure_value_data_absent_reason
+        return unless is_blood_pressure?
+
+        pattern = /component(:[^.]+)?\.dataAbsentReason/
+
+        @must_supports[:elements].delete_if do |element|
+          element[:path].start_with?('value[x]') ||
+            element[:original_path]&.start_with?('value[x]') ||
+            element[:path] == ('dataAbsentReason') ||
+            (
+              pattern.match?(element[:path]) && ['3.1.1', '4.0.0'].include?(ig_resources.ig.version)
+            )
+        end
+
+        @must_supports[:slices].delete_if do |slice|
+          slice[:path].start_with?('value[x]')
+        end
+      end
+
+      # ONC and US Core 4.0.0 both clarified that health IT developers that always provide HL7 FHIR "observation" values
+      # are not required to demonstrate Health IT Module support for "dataAbsentReason" elements.
+      # Remove MS check for dataAbsentReason and component.dataAbsentReason from vital sign profiles and observation lab profile
+      # Smoking status profile does not have MS on dataAbsentReason. It is safe to use profile.type == 'Observation'
+      # Since US Core 5.0.1, Blood Pressure profile restores component.dataAbsentReason as MustSupport.
+      def remove_observation_data_absent_reason
+        return if is_blood_pressure?
+
+        pattern = /(component(:[^.]+)?\.)?dataAbsentReason/
+
+        return unless profile.type == 'Observation'
+
+        @must_supports[:elements].delete_if do |element|
+          pattern.match?(element[:path])
+        end
+      end
+    end
+  end
+end