FI-3440 review feedback, part 1

lib/inferno/apps/cli/evaluate.rb

@@ -1,5 +1,5 @@
 require_relative '../../../inferno/dsl/fhir_evaluation/evaluator'
-require_relative '../../../inferno/dsl/ig'
+require_relative '../../../inferno/entities'
 require_relative '../../utils/ig_downloader'
 
 require 'tempfile'
@@ -12,15 +12,7 @@ class Evaluate < Thor::Group
 
       def evaluate(ig_path, data_path, _log_level)
         validate_args(ig_path, data_path)
-
-        if File.file?(ig_path)
-          ig = Inferno::DSL::IG.from_file(ig_path)
-        else
-          Tempfile.create('package.tgz') do |temp_file|
-            load_ig(ig_path, nil, { force: true }, temp_file.path)
-            ig = Inferno::DSL::IG.from_file(temp_file.path)
-          end
-        end
+        _ig = get_ig(ig_path)
 
         # Rule execution, and result output below will be integrated soon.
 
@@ -45,6 +37,32 @@ def validate_args(ig_path, data_path)
         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, [email protected])
+          # 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)

lib/inferno/entities.rb

@@ -2,6 +2,7 @@
 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'

lib/inferno/entities/ig.rb

@@ -0,0 +1,147 @@
+# frozen_string_literal: true
+
+require 'fhir_models'
+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_path)
+        ig = IG.new({})
+
+        Dir.glob("#{ig_path}/**/*") do |f|
+          next if skip_item?(f, File.directory?(f))
+
+          begin
+            resource = FHIR::Json.from_json(File.read(f))
+            next if resource.nil?
+
+            ig.handle_resource(resource, f)
+          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
+
+        # TODO: consider making these regexes we can iterate over in a single loop
+        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

lib/inferno/repositories/igs.rb

@@ -0,0 +1,9 @@
+require_relative 'in_memory_repository'
+
+module Inferno
+  module Repositories
+    # Repository that deals with persistence for the `IG` entity.
+    class IGs < InMemoryRepository
+    end
+  end
+end

lib/inferno/utils/ig_downloader.rb

@@ -25,7 +25,6 @@ def load_ig(ig_input, idx = nil, thor_config = { verbose: true }, output_path =
         else
           raise StandardError, <<~FAILED_TO_LOAD
             Could not find implementation guide: #{ig_input}
-            Put its package.tgz file directly in #{ig_path}
           FAILED_TO_LOAD
         end
 

spec/inferno/dsl/ig_spec.rb → spec/inferno/entities/ig_spec.rb

@@ -1,4 +1,4 @@
-RSpec.describe Inferno::DSL::IG do
+RSpec.describe Inferno::Entities::IG do
   let(:uscore3_package) { File.expand_path('../../fixtures/uscore311.tgz', __dir__) }
 
   describe '#from_file' do