inferno_core 0.5.3 → 0.5.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: '090f68164e2fc19d1f97f62dd0fb13c12c77eb12c29bb9b528c9b9cb56f48770'
-  data.tar.gz: e239a1702ee11a85229db5355ad7c8a415d71b40018c052bb3e2c972c824d12c
+  metadata.gz: e11d6b274778016418f7189d8ec9e724cf20861c6e03385dc9c302299f198d18
+  data.tar.gz: '09c65484d51b2f7be0a3985b374d51593d59c432ba11c21bd10d54c798ccafa4'
 SHA512:
-  metadata.gz: 2491100649bba23576a442fdeeef561b407e5f7b0b89fbd0827b55ced37e1dcf29c1f5b908c316e44c38301a74d760b5fa8bba4b2cfdf5e039d36fab4c3c181f
-  data.tar.gz: e05eb12863387acecd5782267f25700d3a2e233ed8f581bda98627a76822c33b5e6a1f0ed8e770a6a9d971c88be610453f0aac9a13245b8412f2cb7673431327
+  metadata.gz: 0daf93ce97d8a5a8e9b409200d7c001e4ac49107887db05073399a74795a94b449d3c1eb1d139214c1402e1ea10a954ee1271b80c642909c379cd7bb0ba7a1f0
+  data.tar.gz: 3a70bb18128af1494e0fcd1a023d8e18e8043dd535ae9c00f8471c8eb85e23678fa7c8bcb19591852c3593c6588ba92af206a90644cf6288659179fef98c1a41

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/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/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'