carin_for_blue_button_test_kit 0.9.0

data/lib/carin_for_blue_button_test_kit/generator/group_metadata_extractor.rb

@@ -0,0 +1,240 @@
+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'
+
+module CarinForBlueButtonTestKit
+  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,
+            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
+          }
+
+        #mark_mandatory_and_must_support_searches
+
+        @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
+
+      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('CARIN4BB', "CARIN4BB#{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
+        puts profile.title
+        title = profile.title.gsub(/C4BB\s*/, '').gsub(/\s*Profile/, '').strip
+
+        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, resource, profile_elements)
+      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
+        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') }
+      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
+    end
+  end
+end

data/lib/carin_for_blue_button_test_kit/generator/ig_loader.rb

@@ -0,0 +1,76 @@
+require 'active_support/all'
+require 'fhir_models'
+require 'pathname'
+require 'rubygems/package'
+require 'zlib'
+require_relative 'ig_resources'
+
+module CarinForBlueButtonTestKit
+  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 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."
+            next
+          end
+
+          ig_resources.add(resource)
+        end
+
+        ig_resources
+      end
+    end
+  end
+end

data/lib/carin_for_blue_button_test_kit/generator/ig_metadata.rb

@@ -0,0 +1,50 @@
+module CarinForBlueButtonTestKit
+    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/carin_for_blue_button_test_kit/generator/ig_metadata_extractor.rb

@@ -0,0 +1,40 @@
+require_relative 'ig_metadata'
+require_relative 'group_metadata_extractor'
+
+module CarinForBlueButtonTestKit
+  class Generator
+    class IGMetadataExtractor
+      attr_accessor :ig_resources, :metadata
+
+      def initialize(ig_resources)
+        self.ig_resources = ig_resources
+        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 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/carin_for_blue_button_test_kit/generator/ig_resources.rb

@@ -0,0 +1,50 @@
+module CarinForBlueButtonTestKit
+    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)
+          # remove '_' from search parameter name, such as _id or _tag
+          normalized_name = normalized_name = name.to_s.delete_prefix('_')
+          resources_by_type['SearchParameter']
+            .find { |param| 
+              param.id == "#{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/carin_for_blue_button_test_kit/generator/include_search_test_generator.rb

@@ -0,0 +1,105 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module CarinForBlueButtonTestKit
+  class Generator
+        class IncludeSearchTestGenerator
+
+          attr_accessor :group_metadata, :search_param, :base_output_dir
+
+          def initialize(group_metadata, search_param, base_output_dir)
+            self.group_metadata = group_metadata
+            self.search_param = search_param
+            self.base_output_dir = base_output_dir
+          end
+
+          def include_search
+            true
+          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
+
+          def template
+            @template ||= File.read(File.join(__dir__, 'templates', 'include_search.rb.erb'))
+          end
+
+          def output
+            @output ||= ERB.new(template).result(binding)
+          end
+
+          def output_file_directory
+            File.join(base_output_dir, profile_identifier)
+          end
+
+          def output_file_name
+            File.join(output_file_directory, base_output_file_name)
+          end
+
+          def profile_identifier
+            Naming.snake_case_for_profile(group_metadata)
+          end
+
+          def base_output_file_name
+            "#{class_name.underscore}.rb"
+          end
+
+          def test_id
+            "c4bb_#{group_metadata.reformatted_version}_#{profile_identifier}_include_#{remove_star}_search_test"
+          end
+
+          def module_name
+            "CARIN4BB#{group_metadata.reformatted_version.upcase}"
+          end
+
+          def class_name
+            "#{Naming.upper_camel_case_for_profile(group_metadata)}#{remove_star}SearchTest"
+          end
+
+          def input_id
+            "c4bb_#{group_metadata.reformatted_version}_#{profile_identifier}__id_search_test_param"
+          end
+
+          def input_title
+            "#{resource_type} search parameter for _id"
+          end
+
+          def input_description
+            "#{resource_type} search parameter: _id"
+          end
+
+          def removed_hyphen
+            search_param.gsub('-', '')
+          end
+
+          def remove_colon
+            removed_hyphen.gsub(':', '_')
+          end
+
+          def remove_star
+            remove_colon.gsub('*', 'All')
+          end
+
+          def resource_type
+            group_metadata.resource
+          end
+
+          def include_search_param
+            search_param
+          end
+
+          def description
+            <<~DESCRIPTION
+              Tests that the server responds correctly when using _include="#{search_param}" as a search parameter 
+            DESCRIPTION
+          end
+        end
+    end
+end