us_core_test_kit 0.1.0

data/lib/us_core_test_kit/generator/ig_loader.rb

@@ -0,0 +1,63 @@
+require 'active_support/all'
+require 'fhir_models'
+require 'rubygems/package'
+require 'zlib'
+require_relative 'ig_resources'
+
+module USCoreTestKit
+  class Generator
+    class IGLoader
+      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(File.join(__dir__, '..', 'igs', 'package.tgz')))
+
+        tar.each do |entry|
+          next if entry.directory?
+
+          file_name = entry.full_name.split('/').last
+
+          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
+        Dir.glob(File.join(__dir__, '..', 'igs', '*.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."
+            next
+          end
+
+          ig_resources.add(resource)
+        end
+
+        ig_resources
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/ig_metadata.rb

@@ -0,0 +1,49 @@
+module USCoreTestKit
+  class Generator
+    class IGMetadata
+      attr_accessor :ig_version, :groups
+
+      def reformatted_version
+        @reformatted_version ||= ig_version.delete('.')
+      end
+
+      def ordered_groups
+        @ordered_groups ||=
+          [patient_group] + non_delayed_groups + delayed_groups
+      end
+
+      def patient_group
+        @patient_group ||=
+          groups.find { |group| group.resource == 'Patient' }
+      end
+
+      def delayed_groups
+        @delayed_groups ||=
+          groups.select { |group| group.delayed? }
+      end
+
+      def non_delayed_groups
+        @non_delayed_groups ||=
+          groups.reject { |group| group.delayed? } - [patient_group]
+      end
+
+      def delayed_profiles
+        @delayed_profiles ||=
+          delayed_groups.map(&:profile_url)
+      end
+
+      def postprocess_groups(ig_resources)
+        groups.each do |group|
+          group.add_delayed_references(delayed_profiles, ig_resources)
+        end
+      end
+
+      def to_hash
+        {
+          ig_version: ig_version,
+          groups: groups.map(&:to_hash)
+        }
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/ig_metadata_extractor.rb

@@ -0,0 +1,56 @@
+require_relative 'ig_metadata'
+require_relative 'group_metadata_extractor'
+
+module USCoreTestKit
+  class Generator
+    class IGMetadataExtractor
+      attr_accessor :ig_resources, :metadata
+
+      def initialize(ig_resources)
+        self.ig_resources = ig_resources
+        add_vital_signs_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
+
+      # The US Core Server Capability Statement does not list support for the
+      # required vital signs profiles, so they need to be added
+      def add_vital_signs_profiles
+        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'
+          ]
+      end
+
+      def add_metadata_from_resources
+        metadata.groups =
+          resources_in_capability_statement.flat_map do |resource|
+            resource.supportedProfile&.map do |supported_profile|
+              GroupMetadataExtractor.new(resource, supported_profile, metadata, ig_resources).group_metadata
+            end
+          end
+
+        metadata.postprocess_groups(ig_resources)
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/ig_resources.rb

@@ -0,0 +1,48 @@
+module USCoreTestKit
+  class Generator
+    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 search_param_by_resource_and_name(resource, name)
+        normalized_name = name.to_s == '_id' ? 'id' : name.to_s
+
+        resources_by_type['SearchParameter']
+          .find { |param| param.id == "us-core-#{resource.downcase}-#{normalized_name}" }
+      end
+
+      private
+
+      def resources_by_type
+        @resources_by_type ||= Hash.new { |hash, key| hash[key] = [] }
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -0,0 +1,221 @@
+module USCoreTestKit
+  class Generator
+    class MustSupportMetadataExtractor
+      attr_accessor :profile_elements, :profile, :resource
+
+      def initialize(profile_elements, profile, resource)
+        self.profile_elements = profile_elements
+        self.profile = profile
+        self.resource = resource
+      end
+
+      def must_supports
+        {
+          extensions: must_support_extensions,
+          slices: must_support_slices,
+          elements: must_support_elements
+        }
+      end
+
+      # exclude component from vital sign profiles except observation-bp and observation-pulse-ox
+      # observation-bp is excluded by profile.name != 'observation-bp'
+      # observation-plux-ox is excluded by profile.baseDefinition == 'http://hl7.org/fhir/StructureDefinition/vitalsigns'
+      def vital_signs_component?(element)
+        profile.baseDefinition == 'http://hl7.org/fhir/StructureDefinition/vitalsigns' &&
+          profile.name != 'observation-bp' &&
+          element.path.include?('component')
+      end
+
+      def blood_pressure_value?(element)
+        profile.name == 'observation-bp' && element.path.include?('Observation.value[x]')
+      end
+
+      # ONC 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      
+      def data_absent_reason?(element)
+        profile.type == 'Observation' && ['Observation.dataAbsentReason', 'Observation.component.dataAbsentReason'].include?(element.path)
+      end
+
+      def all_must_support_elements
+        profile_elements
+          .select { |element| element.mustSupport }
+          .reject do |element|
+            # TODO: Can special cases be moved out of here?
+            vital_signs_component?(element) || blood_pressure_value?(element) || data_absent_reason?(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|
+          {
+            id: element.id,
+            url: element.type.first.profile.first
+          }
+        end
+      end
+
+      def must_support_slice_elements
+        all_must_support_elements.select { |element| !element.path.end_with?('extension') && element.sliceName.present? }
+      end
+
+      def sliced_element(slice)
+        profile_elements.find { |element| element.id == slice.path }
+      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|
+          {
+            name: current_element.id,
+            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 == '$this'
+            pattern_element =
+              if discriminator_path.present?
+                profile_elements.find { |element| element.id == "#{current_element.id}.#{discriminator_path}" }
+              else
+                current_element
+              end
+
+            metadata[:discriminator] =
+              if pattern_element.patternCodeableConcept.present?
+                {
+                  type: 'patternCodeableConcept',
+                  path: discriminator_path,
+                  code: pattern_element.patternCodeableConcept.coding.first.code,
+                  system: pattern_element.patternCodeableConcept.coding.first.system
+                }
+              elsif pattern_element.patternIdentifier.present?
+                {
+                  type: 'patternIdentifier',
+                  path: discriminator_path,
+                  system: pattern_element.patternIdentifier.system
+                }
+              else
+                raise StandardError, 'Unsupported discriminator pattern type'
+              end
+          end
+        end
+      end
+
+      def must_support_type_slice_elements
+        must_support_slice_elements.select do |element|
+          discriminators(sliced_element(element)).first.type == 'type'
+        end
+      end
+
+      def type_slices
+        must_support_type_slice_elements.map do |current_element|
+          discriminator = discriminators(sliced_element(current_element)).first
+          type_path = discriminator.path
+          type_path = '' if type_path == '$this'
+          type_element =
+            if type_path.present?
+              elements.find { |element| element.id == "#{current_element.id}.#{type_path}" }
+            else
+              current_element
+            end
+
+          type_code = type_element.type.first.code
+
+          {
+            name: current_element.id,
+            path: current_element.path.gsub("#{resource}.", ''),
+            discriminator: {
+              type: 'type',
+              code: type_code.upcase_first
+            }
+          }
+        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|
+          {
+            name: current_element.id,
+            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
+
+              binding.pry if fixed_element.nil?
+              {
+                path: discriminator.path,
+                value: fixed_element.fixedUri || fixed_element.fixedCode
+              }
+            end
+          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 handle_fixed_values(metadata, element)
+        if element.fixedUri.present?
+          metadata[:fixed_value] = element.fixedUri
+        elsif element.patternCodeableConcept.present?
+          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?
+          metadata[:fixed_value] = element.patternIdentifier.system
+          metadata[:path] += '.system'
+        end
+      end
+
+      def must_support_elements
+        plain_must_support_elements.each_with_object([]) do |current_element, must_support_elements_metadata|
+          {
+            path: current_element.path.gsub("#{resource}.", '')
+          }.tap do |current_metadata|
+            path = current_element.path.gsub("#{resource}.", '')
+            current_metadata[:path] = path
+
+            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.uniq
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/must_support_test_generator.rb

@@ -0,0 +1,86 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module USCoreTestKit
+  class Generator
+    class MustSupportTestGenerator
+      class << self
+        def generate(ig_metadata)
+          ig_metadata.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', 'must_support.rb.erb'))
+      end
+
+      def output
+        @output ||= ERB.new(template).result(binding)
+      end
+
+      def base_output_file_name
+        "#{class_name.underscore}.rb"
+      end
+
+      def output_file_directory
+        File.join(__dir__, '..', 'generated', profile_identifier)
+      end
+
+      def output_file_name
+        File.join(output_file_directory, base_output_file_name)
+      end
+
+      def read_interaction
+        self.class.read_interaction(group_metadata)
+      end
+
+      def profile_identifier
+        Naming.snake_case_for_profile(group_metadata)
+      end
+
+      def test_id
+        "us_core_311_#{profile_identifier}_must_support_test"
+      end
+
+      def class_name
+        "#{Naming.upper_camel_case_for_profile(group_metadata)}MustSupportTest"
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def resource_collection_string
+        'all_scratch_resources'
+      end
+
+      def must_support_list_string
+        slice_names = group_metadata.must_supports[:slices].map { |slice| slice[:name] }
+        element_names = group_metadata.must_supports[:elements].map { |slice| "#{resource_type}.#{slice[:path]}" }
+        extension_names = group_metadata.must_supports[:extensions].map { |slice| slice[:id] }
+        (slice_names + element_names + extension_names)
+          .sort
+          .map { |name| "      * #{name}" }
+          .join("\n")
+      end
+
+      def generate
+        FileUtils.mkdir_p(output_file_directory)
+        File.open(output_file_name, 'w') { |f| f.write(output) }
+
+        group_metadata.add_test(
+          id: test_id,
+          file_name: base_output_file_name
+        )
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/naming.rb

@@ -0,0 +1,58 @@
+module USCoreTestKit
+  class Generator
+    module Naming
+      ALLERGY_INTOLERANCE = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance'
+      CARE_PLAN = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan'
+      CARE_TEAM = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-careteam'
+      CONDITION = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition'
+      IMPLANTABLE_DEVICE = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-implantable-device'
+      DIAGNOSTIC_REPORT_NOTE = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note'
+      DIAGNOSTIC_REPORT_LAB = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-lab'
+      DOCUMENT_REFERENCE = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference'
+      ENCOUNTER = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter'
+      GOAL = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-goal'
+      IMMUNIZATION = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-immunization'
+      LOCATION = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'
+      MEDICATION = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication'
+      MEDICATION_REQUEST = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest'
+      SMOKING_STATUS = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus'
+      PEDIATRIC_WEIGHT_FOR_HEIGHT = 'http://hl7.org/fhir/us/core/StructureDefinition/pediatric-weight-for-height'
+      OBSERVATION_LAB = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab'
+      PEDIATRIC_BMI_FOR_AGE = 'http://hl7.org/fhir/us/core/StructureDefinition/pediatric-bmi-for-age'
+      PULSE_OXIMETRY = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-pulse-oximetry'
+      HEAD_CIRCUMFERENCE = 'http://hl7.org/fhir/us/core/StructureDefinition/head-occipital-frontal-circumference-percentile'
+      ORGANIZATION = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization'
+      PATIENT = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient'
+      PRACTITIONER = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner'
+      PRACTITIONER_ROLE = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole'
+      PROCEDURE = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure'
+      PROVENANCE = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-provenance'
+
+      class << self
+        def resources_with_multiple_profiles
+          ['Observation', 'DiagnosticReport']
+        end
+
+        def resource_has_multiple_profiles?(resource)
+          resources_with_multiple_profiles.include? resource
+        end
+
+        def snake_case_for_profile(group_metadata)
+          resource = group_metadata.resource
+          return resource.underscore unless resource_has_multiple_profiles?(resource)
+
+          return 'head_circumference' if group_metadata.profile_url == HEAD_CIRCUMFERENCE
+
+          group_metadata.name
+            .delete_prefix('us_core_')
+            .gsub('diagnosticreport', 'diagnostic_report')
+            .underscore
+        end
+
+        def upper_camel_case_for_profile(group_metadata)
+          snake_case_for_profile(group_metadata).camelize
+        end
+      end
+    end
+  end
+end