inferno_core 0.6.4 → 0.6.5

data/lib/inferno/public/bundle.js.LICENSE.txt

@@ -61,7 +61,7 @@
  */
 
 /**
- * @remix-run/router v1.19.2
+ * @remix-run/router v1.21.0
  *
  * Copyright (c) Remix Software Inc.
  *
@@ -72,7 +72,7 @@
  */
 
 /**
- * React Router DOM v6.26.2
+ * React Router DOM v6.28.1
  *
  * Copyright (c) Remix Software Inc.
  *
@@ -83,7 +83,7 @@
  */
 
 /**
- * React Router v6.26.2
+ * React Router v6.28.1
  *
  * Copyright (c) Remix Software Inc.
  *

data/lib/inferno/repositories/igs.rb

@@ -1,9 +1,131 @@
 require_relative 'in_memory_repository'
 
+require_relative '../utils/ig_downloader'
+
 module Inferno
   module Repositories
     # Repository that deals with persistence for the `IG` entity.
     class IGs < InMemoryRepository
+      include Inferno::Utils::IgDownloader
+
+      # Get the instance of the IG specified by either identifier or file path.
+      # An in-memory instance will be returned if already loaded, otherwise
+      # the IG will be retrieved from the user package cache (~/.fhir/packages)
+      # or from the package server and then loaded into the repository.
+      # @param id_or_path [String] either an identifier, eg "hl7.fhir.us.core#3.1.1"
+      #        or a file path, eg "./igs/uscore.tgz"
+      # @return [Inferno::Entities::IG]
+      def find_or_load(id_or_path)
+        return find(id_or_path) if exists?(id_or_path)
+
+        ig_by_path = find_by_path(id_or_path)
+
+        return ig_by_path if ig_by_path
+
+        load(id_or_path)
+      end
+
+      # Get the instance of the already-loaded IG specified by file path.
+      # @param path [String] file path, eg "./igs/uscore.tgz"
+      # @return [Inferno::Entities::IG]
+      def find_by_path(path)
+        all.find { |ig| ig.source_path == path }
+      end
+
+      # @private
+      def load(ig_path)
+        local_ig_file = find_local_file(ig_path)
+        if local_ig_file
+          ig = Inferno::Entities::IG.from_file(local_ig_file)
+          # To match the HL7 FHIR validator, DO NOT cache igs loaded from file
+        elsif in_user_package_cache?(ig_path.sub('@', '#'))
+          # NPM syntax for a package identifier is id@version (eg, hl7.fhir.us.core@3.1.1)
+          # but in the cache the separator is # (hl7.fhir.us.core#3.1.1)
+          cache_directory = File.join(user_package_cache, ig_path.sub('@', '#'))
+          ig = Inferno::Entities::IG.from_file(cache_directory)
+        else
+          Tempfile.create(['package', '.tgz']) do |temp_file|
+            load_ig(ig_path, nil, temp_file.path)
+            cache_directory = add_package_to_cache(ig_path.sub('@', '#'), temp_file.path)
+            ig = Inferno::Entities::IG.from_file(cache_directory)
+          end
+        end
+        ig.add_self_to_repository
+        ig
+      end
+
+      # @private
+      def find_local_file(ig_path)
+        return nil unless ['.tgz', '.tar.gz'].any? { |ext| ig_path.downcase.end_with?(ext) }
+
+        return ig_path if File.exist?(ig_path)
+
+        # IG packages are copied to ./data/igs to be used by the validator,
+        # and if referenced by file in the validator block the path given must be "igs/{filename}.tgz"
+        data_igs_path = File.join('data', ig_path)
+        return data_igs_path if File.exist?(data_igs_path)
+
+        # Last resort, try to find the file under the current working directory,
+        # eg, given ig_path: 'igs/package123.tgz'
+        # this would find 'lib/my_test_kit/igs/package123.tgz'
+        Dir.glob(File.join('**', ig_path))[0]
+      end
+
+      # @private
+      def user_package_cache
+        File.join(Dir.home, '.fhir', 'packages')
+      end
+
+      # @private
+      def in_user_package_cache?(ig_identifier)
+        File.directory?(File.join(user_package_cache, ig_identifier))
+      end
+
+      # @private
+      def add_package_to_cache(ig_identifier, temp_tgz)
+        return temp_tgz if ENV['READ_ONLY_FHIR_PACKAGE_CACHE'].present?
+
+        # In the HL7 FHIR validator, this is handled by the FilesystemPackageCacheManager:
+        # https://github.com/hapifhir/org.hl7.fhir.core/blob/3cf2a06e7abda7dc32cdc052d3a356c1201139cf/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java#L558
+        # We try to follow the same approach here
+
+        lockfile_path = File.join(user_package_cache, "#{ig_identifier}.lock")
+        lockfile = File.open(lockfile_path, 'w+')
+        lockfile.flock(File::LOCK_EX)
+
+        target_cache_dir = File.join(user_package_cache, ig_identifier)
+
+        # Break early 1 - something else already created it while we got the lock
+        return target_cache_dir if in_user_package_cache?(ig_identifier)
+
+        # 1. Extract to a temp folder under the cache
+        temp_dir = File.join(user_package_cache, SecureRandom.uuid)
+        FileUtils.mkdir_p(temp_dir)
+
+        system "tar -xzf #{temp_tgz} --directory #{temp_dir}"
+
+        # Break early 2 - something else already created it
+        return target_cache_dir if in_user_package_cache?(ig_identifier)
+
+        # 2. Rename the temp folder to the correct name
+        File.rename(temp_dir, target_cache_dir)
+
+        # return the path in cache
+        target_cache_dir
+      rescue StandardError => e
+        Application['logger'].error(e.full_message)
+        # Don't leave a half extracted package behind
+        FileUtils.remove_dir(temp_dir, true)
+
+        # Return the tgz so that processing can continue
+        temp_tgz
+      ensure
+        if lockfile.present?
+          lockfile.flock(File::LOCK_UN)
+          lockfile.close
+          File.delete(lockfile)
+        end
+      end
     end
   end
 end

data/lib/inferno/repositories/in_memory_repository.rb

@@ -16,6 +16,13 @@ module Inferno
         entity
       end
 
+      def remove(entity)
+        return unless exists?(entity.id)
+
+        all.delete(entity)
+        all_by_id.delete(entity.id.to_s)
+      end
+
       def find(id)
         all_by_id[id.to_s]
       end

data/lib/inferno/utils/ig_downloader.rb

@@ -1,3 +1,5 @@
+require 'open-uri'
+
 module Inferno
   module Utils
     module IgDownloader
@@ -14,7 +16,7 @@ module Inferno
         File.join(ig_path, suffix ? "package_#{suffix}.tgz" : 'package.tgz')
       end
 
-      def load_ig(ig_input, idx = nil, thor_config = { verbose: true }, output_path = nil)
+      def load_ig(ig_input, idx = nil, output_path = nil)
         case ig_input
         when FHIR_PACKAGE_NAME_REG_EX
           uri = ig_registry_url(ig_input)
@@ -29,19 +31,28 @@ module Inferno
         end
 
         destination = output_path || ig_file(idx)
-        # use Thor's get to support CLI options config
-        get(uri, destination, thor_config)
+        download_file(uri, destination)
         uri
       end
 
+      def download_file(uri, destination)
+        # Inspired by Thor `get`
+        # https://github.com/rails/thor/blob/3178667e1727504bf4fb693bf4ac74a5ca6c691e/lib/thor/actions/file_manipulation.rb#L81
+        download = URI.send(:open, uri)
+        IO.copy_stream(download, destination)
+      end
+
       def ig_registry_url(ig_npm_style)
-        unless ig_npm_style.include? '@'
+        if ig_npm_style.include?('@')
+          package_name, version = ig_npm_style.split('@')
+        elsif ig_npm_style.include?('#')
+          package_name, version = ig_npm_style.split('#')
+        else
           raise StandardError, <<~NO_VERSION
-            No IG version specified for #{ig_npm_style}; you must specify one with '@'. I.e: hl7.fhir.us.core@6.1.0
+            No IG version specified for #{ig_npm_style}; you must specify one with '@' or '#'. I.e: hl7.fhir.us.core@6.1.0
           NO_VERSION
         end
 
-        package_name, version = ig_npm_style.split('@')
         "https://packages.fhir.org/#{package_name}/-/#{package_name}-#{version}.tgz"
       end
 

data/lib/inferno/version.rb

@@ -1,4 +1,4 @@
 module Inferno
   # Standard patterns for gem versions: https://guides.rubygems.org/patterns/
-  VERSION = '0.6.4'.freeze
+  VERSION = '0.6.5'.freeze
 end

data/spec/shared/test_kit_examples.rb

@@ -70,6 +70,62 @@ RSpec.shared_examples 'platform_deployable_test_kit' do
 
       expect(dockerfile_contents.lines.first.chomp).to eq('FROM ruby:3.3.6')
     end
+
+    context 'when it contains a validator service' do
+      it 'has a data/igs/.keep file' do
+        docker_compose_file_path = File.join(base_path, 'docker-compose.background.yml')
+        docker_compose_contents = YAML.load_file(docker_compose_file_path)
+
+        validator_service_images = [
+          'infernocommunity/fhir-validator-service',
+          'infernocommunity/inferno-resource-validator'
+        ]
+        validator_service =
+          docker_compose_contents['services']
+            .any? { |_name, service| validator_service_images.include? service['image'] }
+
+        if validator_service.present?
+          igs_keep_file = File.join(base_path, 'data', 'igs', '.keep')
+          error_message =
+            "Create a 'data/igs/.keep' file and commit it"
+          expect(File.exist?(igs_keep_file)).to be(true), error_message
+        end
+      end
+
+      it 'uses data/igs as the path for test kit IGs in the hl7 validator service' do
+        docker_compose_file_path = File.join(base_path, 'docker-compose.background.yml')
+        docker_compose_contents = YAML.load_file(docker_compose_file_path)
+
+        hl7_validator_service =
+          docker_compose_contents['services']
+            .find { |_name, service| service['image'] == 'infernocommunity/inferno-resource-validator' }
+        if hl7_validator_service.present?
+          hl7_validator_ig_volume =
+            hl7_validator_service[1]['volumes']&.find { |volume| volume.end_with? 'igs' }
+
+          expected_hl7_validator_volume = './data/igs:/app/igs'
+          error_message =
+            "Update the hl7 validator service IG volume from '#{hl7_validator_ig_volume}' " \
+            "to '#{expected_hl7_validator_volume}'"
+          expect(hl7_validator_ig_volume).to eq(expected_hl7_validator_volume), error_message
+        end
+
+        standalone_validator_service =
+          docker_compose_contents['services']
+            .find { |_name, service| service['image'] == 'infernocommunity/fhir-validator-service' }
+
+        if standalone_validator_service.present?
+          standalone_validator_ig_volume =
+            standalone_validator_service[1]['volumes']&.find { |volume| volume.end_with? 'igs' }
+
+          expected_standalone_validator_volume = './data/igs:/home/igs'
+          error_message =
+            "Update the validator service IG volume from '#{standalone_validator_ig_volume}' " \
+            "to '#{expected_standalone_validator_volume}'"
+          expect(standalone_validator_ig_volume).to eq(expected_standalone_validator_volume), error_message
+        end
+      end
+    end
   end
 
   describe 'suites' do
@@ -99,6 +155,19 @@ RSpec.shared_examples 'platform_deployable_test_kit' do
         expect(link_labels).to include(*expected_labels), error_message
       end
     end
+
+    it 'does not rely on the deprecated `Inferno::DSL::FHIRValidation`' do
+      suites.each do |suite|
+        suite.fhir_validators.each do |name, validators|
+          validators.each do |validator|
+            error_message =
+              "Validator '#{name}' in Suite '#{suite.id}' should be changed to a " \
+              'fhir_resource_validator'
+            expect(validator).to_not be_an_instance_of(Inferno::DSL::FHIRValidation::Validator), error_message
+          end
+        end
+      end
+    end
   end
 
   describe 'presets' do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: inferno_core
 version: !ruby/object:Gem::Version
-  version: 0.6.4
+  version: 0.6.5
 platform: ruby
 authors:
 - Stephen MacVicar
@@ -10,7 +10,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2025-02-14 00:00:00.000000000 Z
+date: 2025-03-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -441,6 +441,7 @@ files:
 - lib/inferno/apps/cli/templates/config/nginx.conf.tt
 - lib/inferno/apps/cli/templates/config/puma.rb.tt
 - lib/inferno/apps/cli/templates/data/.keep
+- lib/inferno/apps/cli/templates/data/igs/.keep
 - lib/inferno/apps/cli/templates/data/redis/.keep
 - lib/inferno/apps/cli/templates/docker-compose.background.yml.tt
 - lib/inferno/apps/cli/templates/docker-compose.yml.tt
@@ -501,6 +502,7 @@ files:
 - lib/inferno/config/boot.rb
 - lib/inferno/config/boot/db.rb
 - lib/inferno/config/boot/executor.rb
+- lib/inferno/config/boot/ig_files.rb
 - lib/inferno/config/boot/logging.rb
 - lib/inferno/config/boot/presets.rb
 - lib/inferno/config/boot/sidekiq.rb
@@ -546,6 +548,7 @@ files:
 - lib/inferno/dsl/jwks.rb
 - lib/inferno/dsl/links.rb
 - lib/inferno/dsl/messages.rb
+- lib/inferno/dsl/must_support_assessment.rb
 - lib/inferno/dsl/must_support_metadata_extractor.rb
 - lib/inferno/dsl/oauth_credentials.rb
 - lib/inferno/dsl/primitive_type.rb