inferno_core 0.5.3 → 0.6.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: '090f68164e2fc19d1f97f62dd0fb13c12c77eb12c29bb9b528c9b9cb56f48770'
-  data.tar.gz: e239a1702ee11a85229db5355ad7c8a415d71b40018c052bb3e2c972c824d12c
+  metadata.gz: ee348703cfa562d9316b03c470d62aebd0d4ac232d8dc6029bbac392cb5a64d1
+  data.tar.gz: 666f20e627f22eea29c764f9d10c6a2e421142edd0525631566a678f73ed3a45
 SHA512:
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-  data.tar.gz: e05eb12863387acecd5782267f25700d3a2e233ed8f581bda98627a76822c33b5e6a1f0ed8e770a6a9d971c88be610453f0aac9a13245b8412f2cb7673431327
+  metadata.gz: 85323238cd047bd7408aa5e50dcbf8bd7ff4bca02bbc985928627bf5431189bb6cee9f0d660218d7bd0684fb38e0f6bfd49aea164cdd08352c463cadaa30ed58
+  data.tar.gz: 8cd139293bf774f09749cbe3e723df226b2b74b79a3141ae144e09e573afcc8712495d9fa80eb62b901e05f5f0e2c7cc2810ea4b2e47ee70b53571964ad04683

data/lib/inferno/apps/cli/evaluate.rb

@@ -1,14 +1,21 @@
 require_relative '../../../inferno/dsl/fhir_evaluation/evaluator'
+require_relative '../../../inferno/entities'
+require_relative '../../utils/ig_downloader'
+
+require 'tempfile'
 
 module Inferno
   module CLI
-    class Evaluate
-      def run(ig_path, data_path, _log_level)
+    class Evaluate < Thor::Group
+      include Thor::Actions
+      include Inferno::Utils::IgDownloader
+
+      def evaluate(ig_path, data_path, _log_level)
         validate_args(ig_path, data_path)
+        _ig = get_ig(ig_path)
 
-        # IG Import, rule execution, and result output below will be integrated at phase 2 and 3.
+        # Rule execution, and result output below will be integrated soon.
 
-        # @ig = File.join(__dir__, 'ig', ig_path)
         # if data_path
         #   DatasetLoader.from_path(File.join(__dir__, data_path))
         # else
@@ -30,6 +37,32 @@ module Inferno
         raise "Provided path '#{data_path}' is not a directory"
       end
 
+      def get_ig(ig_path)
+        if File.exist?(ig_path)
+          ig = Inferno::Entities::IG.from_file(ig_path)
+        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, { force: true }, temp_file.path)
+            ig = Inferno::Entities::IG.from_file(temp_file.path)
+          end
+        end
+        ig.add_self_to_repository
+        ig
+      end
+
+      def user_package_cache
+        File.join(Dir.home, '.fhir', 'packages')
+      end
+
+      def in_user_package_cache?(ig_identifier)
+        File.directory?(File.join(user_package_cache, ig_identifier))
+      end
+
       def output_results(results, output)
         if output&.end_with?('json')
           oo = FhirEvaluator::EvaluationResult.to_operation_outcome(results)

data/lib/inferno/apps/cli/execute/console_outputter.rb

@@ -51,8 +51,8 @@ module Inferno
 
         # private
 
-        def verbose_print(options, *args)
-          print(color.dim(*args)) if options[:verbose]
+        def verbose_print(options, *)
+          print(color.dim(*)) if options[:verbose]
         end
 
         def color

data/lib/inferno/apps/cli/main.rb

@@ -45,7 +45,7 @@ module Inferno
              type: :string,
              desc: 'Export evaluation result to outcome.json as an OperationOutcome'
       def evaluate(ig_path)
-        Evaluate.new.run(ig_path, options[:data_path], Logger::INFO)
+        Evaluate.new.evaluate(ig_path, options[:data_path], Logger::INFO)
       end
 
       desc 'console', 'Start an interactive console session with Inferno'

data/lib/inferno/apps/cli/new.rb

@@ -71,6 +71,7 @@ module Inferno
         inside(root_name) do
           bundle_install
           inferno_migrate
+          initialize_git_repo
           load_igs
         end
 
@@ -85,7 +86,7 @@ module Inferno
       private
 
       def authors
-        options['author'].presence || [default_author]
+        (options['author'].presence || [default_author]).to_json.gsub('"', "'")
       end
 
       def default_author
@@ -106,6 +107,10 @@ module Inferno
         run 'bundle exec inferno migrate', verbose: !options['quiet'], capture: options['quiet']
       end
 
+      def initialize_git_repo
+        run 'git init -q && git add . && git commit -aqm "initial commit"'
+      end
+
       def load_igs
         config = { verbose: !options['quiet'] }
         options['implementation_guide']&.each_with_index do |ig, idx|
@@ -119,8 +124,8 @@ module Inferno
         end
       end
 
-      def say_unless_quiet(*args)
-        say(*args) unless options['quiet']
+      def say_unless_quiet(*)
+        say(*) unless options['quiet']
       end
     end
   end

data/lib/inferno/apps/cli/suites.rb

@@ -6,8 +6,6 @@ module Inferno
       def run
         ENV['NO_DB'] = 'true'
 
-        require_relative '../../../inferno'
-
         Inferno::Application.start(:suites)
 
         suites = Inferno::Repositories::TestSuites.new.all

data/lib/inferno/apps/cli/templates/%library_name%.gemspec.tt

@@ -5,29 +5,18 @@ Gem::Specification.new do |spec|
   spec.version       = <%= module_name %>::VERSION
   spec.authors       = <%= authors %>
   # spec.email         = ['TODO']
-  spec.date          = Time.now.utc.strftime('%Y-%m-%d')
   spec.summary       = '<%= title_name %>'
   # spec.description   = <<~DESCRIPTION
   #   This is a big markdown description of the test kit.
   # DESCRIPTION
   # spec.homepage      = 'TODO'
   spec.license       = 'Apache-2.0'
-  spec.add_runtime_dependency 'inferno_core', '~> <%= Inferno::VERSION %>'
-  spec.add_development_dependency 'database_cleaner-sequel', '~> 1.8'
-  spec.add_development_dependency 'factory_bot', '~> 6.1'
-  spec.add_development_dependency 'rspec', '~> 3.10'
-  spec.add_development_dependency 'webmock', '~> 3.11'
-  spec.required_ruby_version = Gem::Requirement.new('>= 3.1.2')
+  spec.add_dependency 'inferno_core', '~> <%= Inferno::VERSION %>'
+  spec.required_ruby_version = Gem::Requirement.new('>= 3.3.6')
   spec.metadata['inferno_test_kit'] = 'true'
   # spec.metadata['homepage_uri'] = spec.homepage
   # spec.metadata['source_code_uri'] = 'TODO'
-  spec.files = [
-    Dir['lib/**/*.rb'],
-    Dir['lib/**/*.json'],
-    Dir['config/presets/*.json'],
-    Dir['config/presets/*.json.erb'],
-    'LICENSE'
-  ].flatten
+  spec.files         = `[ -d .git ] && git ls-files -z lib config/presets LICENSE`.split("\x0")
 
   spec.require_paths = ['lib']
 end

data/lib/inferno/apps/cli/templates/.rubocop.yml

@@ -0,0 +1,77 @@
+require:
+  - rubocop-rspec
+
+AllCops:
+  NewCops: enable
+  SuggestExtensions: false
+  TargetRubyVersion: 3.3
+  Exclude:
+    - 'Gemfile'
+    - 'vendor/**/*'
+
+Layout/LineLength:
+  Max: 120
+
+Layout/MultilineMethodCallIndentation:
+  EnforcedStyle: 'indented'
+
+Style/Documentation:
+  Enabled: false
+
+Style/FrozenStringLiteralComment:
+  Enabled: false
+
+Style/NumericLiterals:
+  Enabled: false
+
+Style/OpenStructUse:
+  Exclude:
+    - 'spec/**/*'
+
+Style/SymbolArray:
+  Enabled: false
+
+Style/WordArray:
+  Enabled: false
+
+Metrics/AbcSize:
+  Enabled: false
+
+Metrics/BlockLength:
+  Enabled: false
+
+Metrics/ClassLength:
+  Enabled: false
+
+Metrics/MethodLength:
+  Enabled: false
+
+Metrics/ModuleLength:
+  Enabled: false
+
+Metrics/PerceivedComplexity:
+  Enabled: false
+
+Metrics/ParameterLists:
+  Enabled: false
+
+RSpec/AnyInstance:
+  Enabled: false
+
+RSpec/ExampleLength:
+  Enabled: false
+
+RSpec/MultipleExpectations:
+  Enabled: false
+
+RSpec/MultipleMemoizedHelpers:
+  Enabled: false
+
+RSpec/NestedGroups:
+  Enabled: false
+
+RSpec/NotToNot:
+  EnforcedStyle: to_not
+
+Gemspec/RequireMFA:
+  Enabled: false

data/lib/inferno/apps/cli/templates/.ruby-version

@@ -1 +1 @@
-3.1.2
+3.3.6

data/lib/inferno/apps/cli/templates/.tool-versions

@@ -1 +1 @@
-ruby 3.1.2
+ruby 3.3.6

data/lib/inferno/apps/cli/templates/Dockerfile.tt

@@ -1,4 +1,4 @@
-FROM ruby:3.1.2
+FROM ruby:3.3.6
 
 ENV INSTALL_PATH=/opt/inferno/
 ENV APP_ENV=production

data/lib/inferno/apps/cli/templates/Gemfile.tt

@@ -6,8 +6,15 @@ gemspec
 
 group :development, :test do
   gem 'debug'
+  gem 'rubocop', '~> 1.9'
+  gem 'rubocop-rspec', require: false
 end
 
 group :test do
+  gem 'database_cleaner-sequel', '~> 1.8'
+  gem 'factory_bot', '~> 6.1'
   gem 'rack-test'
+  gem 'rspec', '~> 3.10'
+  gem 'simplecov', '0.21.2', require: false
+  gem 'webmock', '~> 3.11'
 end

data/lib/inferno/apps/cli/templates/lib/%library_name%/suite.rb.tt

@@ -56,4 +56,4 @@ module <%= module_name %>
     # using their id
     group from: :patient_group
   end
-end
+end

data/lib/inferno/config/boot/suites.rb

@@ -6,6 +6,7 @@ Inferno::Application.register_provider(:suites) do
     require 'inferno/entities/test_group'
     require 'inferno/entities/test_suite'
     require 'inferno/entities/test_kit'
+    require 'inferno/route_storage'
 
     files_to_load = Dir.glob(File.join(Dir.pwd, 'lib', '*.rb'))
 

data/lib/inferno/dsl/fhir_resource_validation.rb

@@ -380,10 +380,10 @@ module Inferno
         #   using multiple validators
         # @param required_suite_options [Hash] suite options that must be
         #   selected in order to use this validator
-        def fhir_resource_validator(name = :default, required_suite_options: nil, &block)
+        def fhir_resource_validator(name = :default, required_suite_options: nil, &)
           current_validators = fhir_validators[name] || []
 
-          new_validator = Inferno::DSL::FHIRResourceValidation::Validator.new(name, id, required_suite_options, &block)
+          new_validator = Inferno::DSL::FHIRResourceValidation::Validator.new(name, id, required_suite_options, &)
 
           current_validators.reject! { |validator| validator.requirements == required_suite_options }
           current_validators << new_validator

data/lib/inferno/dsl/fhir_validation.rb

@@ -254,10 +254,10 @@ module Inferno
         #   using multiple validators
         # @param required_suite_options [Hash] suite options that must be
         #   selected in order to use this validator
-        def validator(name = :default, required_suite_options: nil, &block)
+        def validator(name = :default, required_suite_options: nil, &)
           current_validators = fhir_validators[name] || []
 
-          new_validator = Inferno::DSL::FHIRValidation::Validator.new(required_suite_options, &block)
+          new_validator = Inferno::DSL::FHIRValidation::Validator.new(required_suite_options, &)
 
           current_validators.reject! { |validator| validator.requirements == required_suite_options }
           current_validators << new_validator

data/lib/inferno/dsl/suite_endpoint.rb

@@ -12,7 +12,7 @@ module Inferno
     #     class AuthorizedEndpoint < Inferno::DSL::SuiteEndpoint
     #       # Identify the incoming request based on a bearer token
     #       def test_run_identifier
-    #         request.header['authorization']&.delete_prefix('Bearer ')
+    #         request.headers['authorization']&.delete_prefix('Bearer ')
     #       end
     #
     #       # Return a json FHIR Patient resource

data/lib/inferno/entities/ig.rb

@@ -0,0 +1,149 @@
+# frozen_string_literal: true
+
+require 'fhir_models'
+require 'pathname'
+require 'rubygems/package'
+require 'zlib'
+
+require_relative '../repositories/igs'
+
+module Inferno
+  module Entities
+    # IG is a wrapper class around the relevant concepts inside an IG.
+    # Not everything within an IG is currently used by Inferno.
+    class IG < Entity
+      ATTRIBUTES = [
+        :id,
+        :profiles,
+        :extensions,
+        :value_sets,
+        :search_params,
+        :examples
+      ].freeze
+
+      include Inferno::Entities::Attributes
+
+      def initialize(**params)
+        super(params, ATTRIBUTES)
+
+        @profiles = []
+        @extensions = []
+        @value_sets = []
+        @examples = []
+        @search_params = []
+      end
+
+      def self.from_file(ig_path)
+        raise "#{ig_path} does not exist" unless File.exist?(ig_path)
+
+        # fhir_models by default logs the entire content of non-FHIR files
+        # which could be things like a package.json
+        original_logger = FHIR.logger
+        FHIR.logger = Logger.new('/dev/null')
+
+        if File.directory?(ig_path)
+          from_directory(ig_path)
+        elsif ig_path.end_with? '.tgz'
+          from_tgz(ig_path)
+        else
+          raise "Unable to load #{ig_path} as it does not appear to be a directory or a .tgz file"
+        end
+      ensure
+        FHIR.logger = original_logger if defined? original_logger
+      end
+
+      def self.from_tgz(ig_path)
+        tar = Gem::Package::TarReader.new(
+          Zlib::GzipReader.open(ig_path)
+        )
+
+        ig = IG.new
+
+        tar.each do |entry|
+          next if skip_item?(entry.full_name, entry.directory?)
+
+          begin
+            resource = FHIR::Json.from_json(entry.read)
+            next if resource.nil?
+
+            ig.handle_resource(resource, entry.full_name)
+          rescue StandardError
+            next
+          end
+        end
+        ig
+      end
+
+      def self.from_directory(ig_directory)
+        ig = IG.new
+
+        ig_path = Pathname.new(ig_directory)
+        Dir.glob("#{ig_path}/**/*") do |f|
+          relative_path = Pathname.new(f).relative_path_from(ig_path).to_s
+          next if skip_item?(relative_path, File.directory?(f))
+
+          begin
+            resource = FHIR::Json.from_json(File.read(f))
+            next if resource.nil?
+
+            ig.handle_resource(resource, relative_path)
+          rescue StandardError
+            next
+          end
+        end
+        ig
+      end
+
+      # These files aren't FHIR resources
+      FILES_TO_SKIP = ['package.json', 'validation-summary.json'].freeze
+
+      def self.skip_item?(relative_path, is_directory)
+        return true if is_directory
+
+        file_name = relative_path.split('/').last
+
+        return true unless file_name.end_with? '.json'
+        return true unless relative_path.start_with? 'package/'
+
+        return true if file_name.start_with? '.' # ignore hidden files
+        return true if file_name.end_with? '.openapi.json'
+        return true if FILES_TO_SKIP.include? file_name
+
+        false
+      end
+
+      def handle_resource(resource, relative_path)
+        case resource.resourceType
+        when 'StructureDefinition'
+          if resource.type == 'Extension'
+            extensions.push resource
+          else
+            profiles.push resource
+          end
+        when 'ValueSet'
+          value_sets.push resource
+        when 'SearchParameter'
+          search_params.push resource
+        when 'ImplementationGuide'
+          @id = extract_package_id(resource)
+        else
+          examples.push(resource) if relative_path.start_with? 'package/example'
+        end
+      end
+
+      def extract_package_id(ig_resource)
+        "#{ig_resource.id}##{ig_resource.version || 'current'}"
+      end
+
+      # @private
+      def add_self_to_repository
+        repository.insert(self)
+      end
+
+      # @private
+      def repository
+        Inferno::Repositories::IGs.new
+      end
+    end
+  end
+end

data/lib/inferno/entities.rb

@@ -2,6 +2,7 @@ require_relative 'entities/attributes'
 require_relative 'entities/has_runnable'
 require_relative 'entities/entity'
 require_relative 'entities/header'
+require_relative 'entities/ig'
 require_relative 'entities/message'
 require_relative 'entities/request'
 require_relative 'entities/result'