au_ps_inferno 0.1.0

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data/LICENSE

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data/lib/au_ps_inferno/generator/constants.rb

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+# frozen_string_literal: true
+
+class Generator
+  # Constants used by the test generator for AU PS (Australian Patient Summary) Inferno.
+  module Constants
+    # Required AU PS FHIR profile URLs. Resources using these profiles must be present
+    # for a valid patient summary.
+    # @return [Array<String>]
+    REQUIRED_PROFILES = %w[
+      http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-bundle
+      http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-composition
+      http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-patient
+      http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-condition
+      http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-allergyintolerance
+      http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-medicationstatement
+      http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-medicationrequest
+    ].freeze
+
+    # Mapping from resource/profile (resourceType|profileUrl) to
+    # an array of filters which restrict entries
+    # for that resource type in section validation.
+    #
+    # Each filter is a hash specifying a FHIRPath 'path' and required 'value'.
+    # The value can be a single value or an array of possible values.
+    #
+    # @return [Hash{String => Array<Hash{String => Object}>}]
+    RESOURCES_FILTERS_MAPPING = {
+      'Observation|http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-diagnosticresult-path' => [
+        { 'path' => 'category.coding.code', 'value' => 'laboratory' }
+      ],
+      'Observation|http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-results-radiology-uv-ips' => [
+        { 'path' => 'category.coding.code', 'value' => 'imaging' }
+      ],
+      'Observation|http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-pregnancy-status-uv-ips' => [
+        { 'path' => 'code.coding.code', 'value' => '82810-3' }
+      ],
+      'Observation|http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-pregnancy-outcome-uv-ips' => [
+        {
+          'path' => 'code.coding.code',
+          'value' => %w[
+            11636-8
+            11637-6
+            11638-4
+            11639-2
+            11640-0
+            11612-9
+            11613-7
+            11614-5
+            33065-4
+          ]
+        }
+      ],
+      'Observation|http://hl7.org.au/fhir/ps/StructureDefinition/au-ps-smokingstatus' => [
+        { 'path' => 'code.coding.code', 'value' => '1747861000168109' }
+      ],
+      'Observation|http://hl7.org/fhir/uv/ips/StructureDefinition/Observation-alcoholuse-uv-ips' => [
+        { 'path' => 'code.coding.code', 'value' => '74013-4' }
+      ]
+    }.freeze
+  end
+end

data/lib/au_ps_inferno/generator/generator.rb

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+# frozen_string_literal: true
+
+require 'fhir_models'
+require 'fileutils'
+require 'yaml'
+require_relative '../utils/inferno_suite_generator_compat'
+
+require_relative 'ig_resources_extractor'
+require_relative 'metadata_manager'
+require_relative 'naming'
+require_relative 'sections_validation_group_generator'
+require_relative 'test_file_generator'
+require_relative 'generator_group_based_metadata_module'
+
+# Generator for test suites targeting AU PS and IPS implementation guides.
+#
+# This class automates extraction and persistence of IG resource metadata for use in test suite
+# generation, including support for additional FHIR resource folders.
+#
+# @example Basic usage
+#   generator = Generator.new('/path/to/ig')
+#   generator.generate
+#
+# @example With extra folder containing additional FHIR resources (e.g. extra StructureDefinitions)
+#   generator = Generator.new('/path/to/ig', additional_resources_path: 'path/to/extra-ig-resources')
+#   generator.generate
+#
+class Generator
+  SyntheticCapability = Struct.new(
+    :type, :interaction, :operation, :searchParam, :searchInclude, :searchRevInclude, :extension
+  )
+
+  include Naming
+  include GeneratorGroupBasedMetadataModule
+
+  def initialize(ig_path, additional_resources_path: nil)
+    register_inferno_suite_generator_config
+    @resources_manager = IGResourcesExtractor.new(
+      ig_path,
+      additional_resources_path: additional_resources_path
+    )
+    @metadata = MetadataManager.new(@resources_manager.ig_resources)
+    @new_metadata = build_new_metadata
+  end
+
+  def generate
+    @resources_manager.extract
+    save_metadata_to_version_folder
+    update_ig_version_rb(@resources_manager.ig_version)
+  end
+
+  private
+
+  def update_ig_version_rb(version)
+    return if version.nil? || version.empty?
+
+    version_rb_path = File.expand_path(File.join('lib', 'au_ps_inferno', 'version.rb'))
+    content = File.read(version_rb_path)
+    updated = content.gsub(/IG_VERSION = '.*'/) { "IG_VERSION = '#{version}'" }
+    if updated == content
+      puts "Warning: IG_VERSION pattern not found in #{version_rb_path}; version was not updated."
+      return
+    end
+    File.write(version_rb_path, updated)
+  end
+
+  def save_metadata_to_version_folder
+    metadata_path = File.join(File.expand_path(File.join('lib', 'au_ps_inferno')), 'metadata.yaml')
+    FileUtils.mkdir_p(File.dirname(metadata_path))
+    @metadata.initiate_build
+    old_metadata = @metadata.metadata_to_dump
+    new_metadata = @new_metadata&.to_hash || {}
+    merged_metadata = merge_metadata_values(old_metadata, new_metadata)
+    File.write(metadata_path, YAML.dump(merged_metadata))
+  end
+end

data/lib/au_ps_inferno/generator/generator_group_based_metadata_module.rb

@@ -0,0 +1,113 @@
+# frozen_string_literal: true
+
+class Generator
+  # Module for building group-based metadata
+  module GeneratorGroupBasedMetadataModule
+    private
+
+    def build_new_metadata
+      config_keeper = Registry.get(:config_keeper)
+      return nil unless config_keeper
+
+      ig_resources = InfernoSuiteGenerator::Generator::IGLoader.new(config_keeper.ig_deps_path).load
+      if ig_resources.cs_resources.present?
+        return InfernoSuiteGenerator::Generator::IGMetadataExtractor.new(ig_resources).extract
+      end
+
+      build_new_metadata_without_capability_statement(ig_resources, config_keeper)
+    end
+
+    def build_new_metadata_without_capability_statement(ig_resources, config_keeper)
+      ig_metadata = build_ig_metadata_base(config_keeper)
+      groups = synthetic_profile_groups(ig_resources, ig_metadata)
+      ig_metadata.groups = groups
+      ig_metadata.postprocess_groups(ig_resources)
+      ig_metadata
+    end
+
+    def build_ig_metadata_base(config_keeper)
+      ig_metadata = InfernoSuiteGenerator::Generator::IGMetadata.new
+      ig_metadata.ig_version = "v#{config_keeper.version}"
+      ig_metadata.ig_id = config_keeper.id
+      ig_metadata.ig_title = config_keeper.title
+      ig_metadata.ig_module_name_prefix = config_keeper.module_name_prefix
+      ig_metadata.ig_test_id_prefix = config_keeper.test_id_prefix
+      ig_metadata
+    end
+
+    def synthetic_profile_groups(ig_resources, ig_metadata)
+      au_ps_profiles(ig_resources).filter_map do |profile|
+        capability = synthetic_resource_capability(profile)
+        InfernoSuiteGenerator::Generator::GroupMetadataExtractor.new(
+          capability, profile.url, ig_metadata, ig_resources
+        ).group_metadata
+      rescue StandardError => e
+        warn "Skipping profile #{profile.url}: #{e.message}"
+        nil
+      end
+    end
+
+    def au_ps_profiles(ig_resources)
+      ig_resources
+        .get_resources_by_type('StructureDefinition')
+        .select { |profile| profile.url.to_s.start_with?('http://hl7.org.au/fhir/ps/StructureDefinition/') }
+        .reject { |profile| profile.type == 'Extension' || profile.snapshot.blank? }
+    end
+
+    def synthetic_resource_capability(profile)
+      SyntheticCapability.new(
+        type: profile.type,
+        interaction: [],
+        operation: [],
+        searchParam: [],
+        searchInclude: [],
+        searchRevInclude: [],
+        extension: []
+      )
+    end
+
+    def register_inferno_suite_generator_config
+      return if Registry.get(:config_keeper)
+
+      config_path = inferno_suite_generator_config_path
+      return unless config_path
+
+      keeper = InfernoSuiteGenerator::Generator::GeneratorConfigKeeper.new([config_path])
+      Registry.register(:config_keeper, keeper)
+    rescue StandardError => e
+      warn "Failed to register inferno_suite_generator config: #{e.message}"
+      nil
+    end
+
+    def inferno_suite_generator_config_path
+      config_paths = [
+        File.expand_path('../../../inferno_suite_generator.config.json', __dir__),
+        File.expand_path('../../../../inferno_suite_generator.config.json', __dir__)
+      ]
+      config_paths.find { |path| File.exist?(path) }
+    end
+
+    def merge_metadata_values(old_value, new_value)
+      return old_value if new_value.nil?
+      return new_value if old_value.nil?
+
+      if old_value.is_a?(Hash) && new_value.is_a?(Hash)
+        merge_metadata_hashes(old_value, new_value)
+      elsif old_value.is_a?(Array) && new_value.is_a?(Array)
+        merge_metadata_arrays(old_value, new_value)
+      else
+        old_value
+      end
+    end
+
+    def merge_metadata_hashes(old_hash, new_hash)
+      (old_hash.keys | new_hash.keys).to_h do |key|
+        [key, merge_metadata_values(old_hash[key], new_hash[key])]
+      end
+    end
+
+    def merge_metadata_arrays(old_array, new_array)
+      old_array + new_array.reject { |item| old_array.include?(item) }
+    end
+  end
+end

data/lib/au_ps_inferno/generator/ig_resources_extractor.rb

@@ -0,0 +1,149 @@
+# frozen_string_literal: true
+
+require 'zlib'
+require 'rubygems/package'
+require 'fhir_models'
+
+class Generator
+  # Extracts FHIR resources from an Implementation Guide (IG) package archive
+  # and optionally from a folder of additional JSON resources.
+  #
+  # Reads a .tar.gz (or .tgz) package, parses JSON entries that represent FHIR
+  # resources (excluding OpenAPI JSON), and populates {#ig_resources} with
+  # FHIR model instances. If +additional_resources_path+ is set, all +.json+
+  # files from that folder (and subfolders) are loaded after the package,
+  # so you can supply missing StructureDefinitions, SearchParameters, etc.
+  #
+  # @example
+  #   extractor = IGResourcesExtractor.new('path/to/package.tar.gz')
+  #   extractor.extract
+  #   extractor.ig_resources # => [FHIR::Patient, ...]
+  #
+  # @example With additional folder
+  #   extractor = IGResourcesExtractor.new('path/to/package.tar.gz', additional_resources_path: 'path/to/extra')
+  #   extractor.extract
+  class IGResourcesExtractor
+    # @return [Array<FHIR::Model>] FHIR resources extracted from the IG package and optional folder
+    attr_reader :ig_resources, :ig_version
+
+    # @param ig_path [String] Path to the IG package file (.tar.gz or .tgz)
+    # @param additional_resources_path [String, nil] Optional path to a folder of JSON FHIR resources
+    #   (e.g. StructureDefinition, SearchParameter) to load in addition to the package.
+    def initialize(ig_path, additional_resources_path: nil)
+      @ig_path = ig_path
+      @additional_resources_path = additional_resources_path
+      @ig_resources = []
+      @ig_version = nil
+    end
+
+    # Processes the package archive and optional folder, and populates {#ig_resources}.
+    # Handles gzip/tar errors and prints messages to stdout on failure.
+    #
+    # @return [void]
+    def extract
+      process_package_archive
+      load_additional_resources_from_folder if @additional_resources_path
+    end
+
+    private
+
+    # Opens the gzipped tar archive and iterates over tar entries.
+    # @return [void]
+    def process_package_archive
+      Zlib::GzipReader.open(@ig_path) do |gz|
+        Gem::Package::TarReader.new(gz) { |tar| process_tar(tar) }
+      end
+    rescue Zlib::GzipFile::Error => e
+      puts_archive_error('gzip', e)
+    rescue Gem::Package::TarInvalidError => e
+      puts_archive_error('tar', e)
+    rescue StandardError => e
+      puts "Error processing archive at #{@ig_path}: #{e.message}"
+    end
+
+    # @param format_type [String] e.g. "gzip" or "tar"
+    # @param error [StandardError] the raised exception
+    # @return [void]
+    def puts_archive_error(format_type, error)
+      msg = "The file at #{@ig_path} is not a valid #{format_type} archive."
+      puts "Error: #{msg} Please ensure it is a valid .tar.gz or .tgz archive."
+      puts "Error details: #{error.message}"
+    end
+
+    # @param tar [Gem::Package::TarReader]
+    # @return [void]
+    def process_tar(tar)
+      tar.each do |entry|
+        if entry.file? && entry.full_name.delete_prefix('./') == 'package/package.json'
+          extract_ig_version(entry)
+          next
+        end
+        next unless relevant_json_entry?(entry)
+
+        collect_resource_from_entry(entry)
+      end
+    end
+
+    # @param entry [Gem::Package::TarReader::Entry]
+    # @return [void]
+    def extract_ig_version(entry)
+      json = JSON.parse(entry.read)
+      @ig_version = json['version']&.to_s
+    rescue StandardError => e
+      puts "Error reading IG version from package.json: #{e.message}"
+    end
+
+    # @param entry [Gem::Package::TarReader::Entry]
+    # @return [Boolean] true if entry is a JSON file and not an OpenAPI JSON
+    def relevant_json_entry?(entry)
+      entry.file? &&
+        entry.full_name.end_with?('.json') &&
+        !entry.full_name.end_with?('.openapi.json')
+    end
+
+    # Parses entry content as JSON and appends a FHIR resource to {#ig_resources} if valid.
+    # @param entry [Gem::Package::TarReader::Entry]
+    # @return [void]
+    def collect_resource_from_entry(entry)
+      content = entry.read
+      json = JSON.parse(content)
+      return unless json.is_a?(Hash) && json['resourceType']
+
+      @ig_resources << FHIR.from_contents(content)
+    rescue StandardError => e
+      puts "Error processing #{entry.full_name}: #{e.message}"
+    end
+
+    # Loads all .json files from {#additional_resources_path} (and subfolders) into {#ig_resources}.
+    # Skips OpenAPI JSON files. Same validation as package entries: must be a Hash with resourceType.
+    # @return [void]
+    def load_additional_resources_from_folder
+      path = File.expand_path(@additional_resources_path)
+      unless File.directory?(path)
+        puts "Error: additional resources path is not a directory: #{path}"
+        return
+      end
+
+      Dir.glob(File.join(path, '**', '*.json')).each do |file_path|
+        next if file_path.end_with?('.openapi.json')
+
+        collect_resource_from_file(file_path)
+      end
+    end
+
+    # @param file_path [String] Absolute path to a JSON file
+    # @return [void]
+    def collect_resource_from_file(file_path)
+      content = File.read(file_path)
+      json = JSON.parse(content)
+      return unless json.is_a?(Hash) && json['resourceType']
+
+      resource = FHIR.from_contents(content)
+      puts "Resource: #{resource.resourceType} with ID: #{resource.id} is loaded from #{file_path}"
+
+      @ig_resources << resource
+    rescue StandardError => e
+      puts "Error processing #{file_path}: #{e.message}"
+    end
+  end
+end