pacio_inferno_core 0.1.0

data/lib/pacio_inferno_core/generator/group_metadata.rb

@@ -0,0 +1,114 @@
+require_relative 'special_cases'
+
+module PacioInfernoCore
+  class Generator
+    class GroupMetadata
+      ATTRIBUTES = %i[
+        name
+        class_name
+        version
+        reformatted_version
+        resource
+        profile_url
+        profile_name
+        profile_version
+        title
+        short_description
+        is_delayed
+        interactions
+        operations
+        searches
+        search_definitions
+        include_params
+        revincludes
+        required_concepts
+        must_supports
+        mandatory_elements
+        bindings
+        references
+        tests
+        granular_scope_tests
+        id
+        file_name
+        delayed_references
+        resource_conformance_expectation
+      ].freeze
+
+      ATTRIBUTES.each { |name| attr_accessor name }
+
+      def initialize(metadata)
+        metadata.each do |key, value|
+          raise "Unknown attribute #{key}" unless ATTRIBUTES.include? key
+
+          instance_variable_set(:"@#{key}", value)
+        end
+      end
+
+      def delayed?
+        @is_delayed ||= if resource == 'Patient'
+                          false
+                        else
+                          no_patient_searches?
+                        end
+      end
+
+      def exclude_search_tests?
+        delayed? && !searchable_delayed_resource?
+      end
+
+      def no_patient_searches?
+        searches.none? { |search| search[:names].include?('patient') && search[:expectation] == 'SHALL' }
+      end
+
+      def optional_profile?
+        SpecialCases::OPTIONAL_PROFILES.key?(profile_url) && SpecialCases::OPTIONAL_PROFILES[profile_url].include?(reformatted_version)
+      end
+
+      def searchable_delayed_resource?
+        SpecialCases::SEARCHABLE_DELAYED_RESOURCES.key?(resource) && SpecialCases::SEARCHABLE_DELAYED_RESOURCES[resource].include?(reformatted_version)
+      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 add_granular_scope_test(id:, file_name:)
+        self.granular_scope_tests ||= []
+
+        self.granular_scope_tests << {
+          id:,
+          file_name:
+        }
+      end
+
+      def to_hash
+        ATTRIBUTES.each_with_object({}) { |key, hash| hash[key] = send(key) unless send(key).nil? }
+      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/pacio_inferno_core/generator/group_metadata_extractor.rb

@@ -0,0 +1,301 @@
+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'
+require_relative 'naming'
+
+module PacioInfernoCore
+  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,
+            profile_version: profile_version,
+            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,
+            resource_conformance_expectation: resource_conformance_expectation
+            # 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|
+            full_paths = search_definitions[name.to_sym][:full_paths]
+            any_must_support_elements = must_supports[:elements].any? do |element|
+              full_must_support_paths = ["#{resource}.#{element[:original_path]}", "#{resource}.#{element[:path]}"]
+
+              full_paths.any? do |path|
+                # allow for non-choice, choice types, and _id
+                name == '_id' || full_must_support_paths.include?(path) || full_must_support_paths.include?("#{path}[x]")
+              end
+            end
+
+            any_must_support_slices = must_supports[:slices].any? do |slice|
+              # only handle type slices because that is all we need for now
+              # for a slice like Observation.effective[x]:effectiveDateTime, the search parameter's expression could be
+              # either Observation.effective or Observation.effectiveDateTime.
+              if slice[:discriminator] && slice[:discriminator][:type] == 'type'
+                full_must_support_path = "#{resource}.#{slice[:path].sub('[x]', slice[:discriminator][:code])}"
+                base_must_support_path = "#{resource}.#{slice[:path].sub('[x]', '')}"
+
+                full_paths.intersection([full_must_support_path, base_must_support_path]).present?
+              else
+                false
+              end
+            end
+
+            any_mandatory_elements = mandatory_elements.any? do |element|
+              full_paths.include?(element)
+            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 ###
+      def category_first_profile?
+        SpecialCases::ALL_VERSION_CATEGORY_FIRST_PROFILES.include?(profile_url) ||
+          SpecialCases::VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES[profile_url]&.include?(reformatted_version)
+      end
+
+      def first_search_params
+        @first_search_params ||=
+          if category_first_profile? 
+            %w[patient category]
+          elsif resource == 'Observation'
+            %w[patient code]
+          elsif resource == 'MedicationRequest'
+            %w[patient intent]
+          elsif resource == 'CareTeam'
+            %w[patient status]
+          else
+            ['patient']
+          end
+      end
+
+      def handle_special_cases
+        set_first_search
+      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 profile_version
+        profile.version
+      end
+
+      def title
+        title = profile.title.gsub(/US\s*Core\s*/, '').gsub(/\s*Profile/, '').strip
+
+        if Naming.resources_with_multiple_profiles.include?(resource) && !title.start_with?(resource) && version != 'v3.1.1'
+          title = resource + ' ' + title.split(resource).map(&:strip).join(' ')
+        end
+
+        title
+      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,
+          profile_elements,
+          {
+            resource: resource,
+            profile_url: profile_url,
+            must_supports: must_supports
+          }
+        )
+      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') }
+          .uniq
+      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, ig_resources)
+      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 }
+            .uniq
+      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
+
+      def resource_conformance_expectation
+        @resource_conformance_expectation ||=
+          resource_capabilities.extension.find do |extension|
+            extension.url == 'http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation'
+          end&.valueCode
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/ig_loader.rb

@@ -0,0 +1,118 @@
+require 'active_support/all'
+require 'fhir_models'
+require 'pathname'
+require 'rubygems/package'
+require 'zlib'
+require_relative 'ig_resources'
+
+module PacioInfernoCore
+  class Generator
+    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? 'openapi.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,tgz}')).each do |file_path|
+          if file_path.end_with? '.tgz'
+            load_tgz_resources(file_path)
+          else
+            load_json_resource(file_path)
+          end
+        end
+
+        ig_resources
+      end
+
+      private
+
+      def load_tgz_resources(file_path)
+        tar = Gem::Package::TarReader.new(
+          Zlib::GzipReader.open(file_path)
+        )
+
+        tar.each do |entry|
+          next if entry.directory?
+
+          file_name = entry.full_name.split('/').last
+
+          next if file_name.end_with? 'openapi.json'
+
+          next if file_name.start_with? 'CapabilityStatement'
+
+          next unless file_name.end_with? '.json'
+
+          next unless entry.full_name.start_with? 'package/'
+
+          # exclude examples from FHIR R4
+          next if file_name.end_with? 'example.json'
+          next if file_name.end_with? 'example-reference.json'
+          next if file_name.end_with? 'example-extension.json'
+
+          load_resource(entry.read, file_name)
+        end
+      end
+
+      def load_json_resource(file_path)
+        load_resource(File.read(file_path), file_path.split('/').last)
+      end
+
+      def load_resource(contents, file_name)
+        begin
+          resource = FHIR.from_contents(contents)
+          return if resource.nil? 
+        rescue StandardError
+          puts "#{file_name} does not appear to be a FHIR resource."
+          return
+        end
+
+        ig_resources.add(resource)
+      end      
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/ig_metadata.rb

@@ -0,0 +1,60 @@
+module PacioInfernoCore
+  class Generator
+    class IGMetadata
+      attr_accessor :ig_version, :groups, :ig_package_id
+
+      def reformatted_version
+        @reformatted_version ||= ig_version.delete('.').gsub('-', '_')
+      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 granular_scope_resource_type_groups
+        @granular_scope_resource_type_groups ||=
+          Hash.new { |hash, key| hash[key] = [] }
+      end
+
+      def granular_scope_groups
+        @granular_scope_groups ||= []
+      end
+
+      def to_hash
+        {
+          ig_version:,
+          groups: groups.map(&:to_hash),
+          granular_scope_resource_type_groups:,
+          granular_scope_groups:
+        }
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/ig_metadata_extractor.rb

@@ -0,0 +1,88 @@
+require_relative 'ig_metadata'
+require_relative 'group_metadata_extractor'
+
+module PacioInfernoCore
+  class Generator
+    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
+        remove_extra_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}".delete('-ballot')
+        metadata.ig_package_id = ig_resources.ig.packageId
+      end
+
+      def resources_in_capability_statement
+        ig_resources.capability_statement.rest.first.resource
+      end
+
+      def add_missing_supported_profiles
+        case ig_resources.ig.version.delete('-ballot')
+        when '3.1.1'
+          # TODO: Remove these after v8.0.0 IG is fixed
+
+          # 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 remove_extra_supported_profiles
+        ig_resources.capability_statement.rest.first.resource
+          .find { |resource| resource.type == 'Observation' }
+          .supportedProfile.delete_if do |profile_url|
+          SpecialCases::PROFILES_TO_EXCLUDE.include?(profile_url)
+        end
+      end
+
+      def add_metadata_from_resources
+        metadata.groups =
+          resources_in_capability_statement.flat_map do |resource|
+            resource.supportedProfile&.map do |supported_profile|
+              # supported_profile = supported_profile.split('|').first
+              next if supported_profile == 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire'
+
+              GroupMetadataExtractor.new(resource, supported_profile, metadata, ig_resources).group_metadata
+            end
+          end.compact
+
+        metadata.postprocess_groups(ig_resources)
+      end
+    end
+  end
+end