inferno_core 0.5.1 → 0.5.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 2266ffdfdf00fea5f565f6b1d5f927ba0c6c64b4d5b5725b737bdb822fe231cd
-  data.tar.gz: bfb17c44e6dabfb9ba46b153e25c1c62aaae6179eaf202505213ab920e4cbcca
+  metadata.gz: '090f68164e2fc19d1f97f62dd0fb13c12c77eb12c29bb9b528c9b9cb56f48770'
+  data.tar.gz: e239a1702ee11a85229db5355ad7c8a415d71b40018c052bb3e2c972c824d12c
 SHA512:
-  metadata.gz: a12e012b24105c8f7e3feb22bd12612ccd4c0f4b345b3289d8fc0c946f1229581f476d1a984418e768b6c0baa65145fcd07f2dd27728ca76508328577de4812b
-  data.tar.gz: f0aabd22881fddc9ad3292e15daf717dd5009fc63d46a947a2696c6d684b11ea239cd669d9e89a0efe0b0eb6233a04fe7e3ae4b8839fb024153a555d7b976fe7
+  metadata.gz: 2491100649bba23576a442fdeeef561b407e5f7b0b89fbd0827b55ced37e1dcf29c1f5b908c316e44c38301a74d760b5fa8bba4b2cfdf5e039d36fab4c3c181f
+  data.tar.gz: e05eb12863387acecd5782267f25700d3a2e233ed8f581bda98627a76822c33b5e6a1f0ed8e770a6a9d971c88be610453f0aac9a13245b8412f2cb7673431327

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

@@ -0,0 +1,64 @@
+require_relative '../../../inferno/dsl/fhir_evaluation/evaluator'
+
+module Inferno
+  module CLI
+    class Evaluate
+      def run(ig_path, data_path, _log_level)
+        validate_args(ig_path, data_path)
+
+        # IG Import, rule execution, and result output below will be integrated at phase 2 and 3.
+
+        # @ig = File.join(__dir__, 'ig', ig_path)
+        # if data_path
+        #   DatasetLoader.from_path(File.join(__dir__, data_path))
+        # else
+        #   ig.examples
+        # end
+
+        # config = Config.new
+        # evaluator = Inferno::DSL::FHIREvaluation::Evaluator.new(data, config)
+
+        # results = evaluate()
+        # output_results(results, options[:output])
+      end
+
+      def validate_args(ig_path, data_path)
+        raise 'A path to an IG is required!' unless ig_path
+
+        return unless data_path && (!File.directory? data_path)
+
+        raise "Provided path '#{data_path}' is not a directory"
+      end
+
+      def output_results(results, output)
+        if output&.end_with?('json')
+          oo = FhirEvaluator::EvaluationResult.to_operation_outcome(results)
+          File.write(output, oo.to_json)
+          puts "Results written to #{output}"
+        else
+          counts = results.group_by(&:severity).transform_values(&:count)
+          print(counts, 'Result Count')
+          puts "\n"
+          puts results
+        end
+      end
+
+      def print(output_fields, title)
+        puts("╔══════════════ #{title} ═══════════════╗")
+        puts('║ ╭────────────────┬──────────────────────╮ ║')
+        output_fields.each_with_index do |(key, value), i|
+          field_name = pad(key, 14)
+          field_value = pad(value.to_s, 20)
+          puts("║ │ #{field_name} │ #{field_value} │ ║")
+          puts('║ ├────────────────┼──────────────────────┤ ║') unless i == output_fields.length - 1
+        end
+        puts('║ ╰────────────────┴──────────────────────╯ ║')
+        puts('╚═══════════════════════════════════════════╝')
+      end
+
+      def pad(string, length)
+        format("%#{length}.#{length}s", string)
+      end
+    end
+  end
+end

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

@@ -44,10 +44,12 @@ module Inferno
 
         self.options = options
 
-        outputter.print_start_message(options)
+        outputter.print_start_message(self.options)
+
+        load_preset_file_and_set_preset_id
 
         results = []
-        outputter.print_around_run(options) do
+        outputter.print_around_run(self.options) do
           if all_selected_groups_and_tests.empty?
             test_run = create_test_run(suite)
             run_one(suite, test_run)
@@ -102,6 +104,18 @@ module Inferno
         @outputter ||= OUTPUTTERS[options[:outputter]].new
       end
 
+      def load_preset_file_and_set_preset_id
+        return unless options[:preset_file]
+        raise StandardError, 'Cannot use `--preset-id` and `--preset-file` options together' if options[:preset_id]
+
+        raise StandardError, "File #{options[:preset_file]} not found" unless File.exist? options[:preset_file]
+
+        options[:preset_id] = JSON.parse(File.read(options[:preset_file]))['id']
+        raise StandardError, "Preset #{options[:preset_file]} is missing id" if options[:preset_id].nil?
+
+        presets_repo.insert_from_file(options[:preset_file])
+      end
+
       def all_selected_groups_and_tests
         @all_selected_groups_and_tests ||= runnables_by_short_id + groups + tests
       end
@@ -109,7 +123,7 @@ module Inferno
       def run_one(runnable, test_run)
         verify_runnable(
           runnable,
-          thor_hash_to_inputs_array(options[:inputs]),
+          thor_hash_to_inputs_array(inputs_and_preset),
           test_session.suite_options
         )
 
@@ -118,6 +132,33 @@ module Inferno
         dispatch_job(test_run)
       end
 
+      def inputs_and_preset
+        if preset
+          preset_inputs = preset.inputs.to_h do |preset_input|
+            [preset_input[:name], preset_input[:value]]
+          end
+
+          options.fetch(:inputs, {}).reverse_merge(preset_inputs)
+        else
+          options.fetch(:inputs, {})
+        end
+      end
+
+      def preset
+        return unless options[:preset_id]
+
+        @preset ||= presets_repo.find(options[:preset_id])
+
+        raise StandardError, "Preset #{options[:preset_id]} not found" if @preset.nil?
+
+        unless presets_repo.presets_for_suite(suite.id).include?(@preset)
+          raise StandardError,
+                "Preset #{options[:preset_id]} is incompatible with suite #{suite.id}"
+        end
+
+        @preset
+      end
+
       def suite
         @suite ||= Inferno::Repositories::TestSuites.new.find(options[:suite])
 
@@ -156,6 +197,10 @@ module Inferno
         @session_data_repo ||= Inferno::Repositories::SessionData.new
       end
 
+      def presets_repo
+        @presets_repo ||= Inferno::Repositories::Presets.new
+      end
+
       def test_session
         @test_session ||= test_sessions_repo.create({
                                                       test_suite_id: suite.id,
@@ -169,7 +214,7 @@ module Inferno
         {
           test_session_id: test_session.id,
           runnable_id_key(runnable) => runnable.id,
-          inputs: thor_hash_to_inputs_array(options[:inputs])
+          inputs: thor_hash_to_inputs_array(inputs_and_preset)
         }
       end
 

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

@@ -1,4 +1,5 @@
 require_relative 'console'
+require_relative 'evaluate'
 require_relative 'migration'
 require_relative 'services'
 require_relative 'suite'
@@ -10,6 +11,43 @@ require_relative 'execute'
 module Inferno
   module CLI
     class Main < Thor
+      desc 'evaluate', 'Run a FHIR Data Evaluator.'
+      long_desc <<-LONGDESC
+        Evaluate FHIR data in the context of a given Implementation Guide,
+        by applying a set of predefined rules designed to check that datasets are comprehensive.
+        Issues identified will be printed to console or to a json file.
+
+        You must have background services running: `bundle exec inferno services start`
+
+        Run the evaluation CLI with
+
+        `bundle exec inferno evaluate ig_path`
+
+        Examples:
+
+        # Load the us core ig and evaluate the data in the provided example folder. If there are examples in the IG already, they will be ignored.
+        `bundle exec inferno evaluate ./uscore.tgz -d ./package/example`
+
+        # Loads the us core ig and evaluate the data included in the IG's example folder
+        `bundle exec inferno evaluate ./uscore.tgz`
+
+        # Loads the us core ig and evaluate the data included in the IG's example folder, with results redirected to outcome.json as an OperationOutcome
+        `bundle exec inferno evaluate ./uscore.tgz --output outcome.json`
+      LONGDESC
+      # TODO: Add options below as arguments
+      option :data_path,
+             aliases: ['-d'],
+             type: :string,
+             desc: 'Example FHIR data path'
+      # TODO: implement option of exporting result as OperationOutcome
+      option :output,
+             aliases: ['-o'],
+             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)
+      end
+
       desc 'console', 'Start an interactive console session with Inferno'
       def console
         Migration.new.run(Logger::INFO)
@@ -125,7 +163,15 @@ module Inferno
       option :inputs,
              aliases: ['-i'],
              type: :hash,
-             desc: 'Inputs (i.e: --inputs=foo:bar goo:baz)'
+             desc: 'Inputs (i.e: --inputs=foo:bar goo:baz); will merge and override preset inputs'
+      option :preset_id,
+             aliases: ['-P'],
+             type: :string,
+             desc: 'Inferno preset id; cannot be used with `--preset-file`'
+      option :preset_file,
+             aliases: ['-p'],
+             type: :string,
+             desc: 'Path to an Inferno preset file for inputs; cannot be used with `--preset-id`'
       option :outputter,
              aliases: ['-o'],
              default: 'console',
@@ -142,7 +188,7 @@ module Inferno
              desc: 'Display this message'
       def execute
         Execute.boot_full_inferno
-        Execute.new.run(options)
+        Execute.new.run(options.dup) # dup to unfreeze Thor options
       end
 
       # https://github.com/rails/thor/issues/244 - Make Thor exit(1) on Errors/Exceptions

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

@@ -1,11 +1,15 @@
+require_relative 'lib/<%= library_name %>/version'
+
 Gem::Specification.new do |spec|
   spec.name          = '<%= library_name %>'
-  spec.version       = '0.0.1'
+  spec.version       = <%= module_name %>::VERSION
   spec.authors       = <%= authors %>
   # spec.email         = ['TODO']
   spec.date          = Time.now.utc.strftime('%Y-%m-%d')
-  spec.summary       = '<%= title_name %> Test Kit'
-  spec.description   = '<%= human_name %> Inferno test kit for FHIR'
+  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 %>'
@@ -14,11 +18,14 @@ Gem::Specification.new do |spec|
   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.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
 

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

@@ -6,12 +6,13 @@ RUN mkdir -p $INSTALL_PATH
 
 WORKDIR $INSTALL_PATH
 
+ADD lib/<%= library_name %>/metadata.rb $INSTALL_PATH/lib/<%= library_name %>/metadata.rb
 ADD *.gemspec $INSTALL_PATH
 ADD Gemfile* $INSTALL_PATH
 RUN gem install bundler
-# The below RUN line is commented out for development purposes, because any change to the 
+# The below RUN line is commented out for development purposes, because any change to the
 # required gems will break the dockerfile build process.
-# If you want to run in Deploy mode, just run `bundle install` locally to update 
+# If you want to run in Deploy mode, just run `bundle install` locally to update
 # Gemfile.lock, and uncomment the following line.
 # RUN bundle config set --local deployment 'true'
 RUN bundle install

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

@@ -0,0 +1,18 @@
+require_relative 'version'
+
+module <%= module_name %>
+  class Metadata < Inferno::TestKit
+    id :<%= test_kit_id %>
+    title '<%= title_name %>'
+    description <<~DESCRIPTION
+      This is a big markdown description of the test kit.
+    DESCRIPTION
+    suite_ids [:<%= test_suite_id %>]
+    # tags ['SMART App Launch', 'US Core']
+    # last_updated '2024-03-07'
+    version VERSION
+    maturity 'Low'
+    authors <%= authors %>
+    # repo 'TODO'
+  end
+end

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

@@ -0,0 +1,59 @@
+require_relative 'metadata'
+require_relative 'patient_group'
+
+module <%= module_name %>
+  class Suite < Inferno::TestSuite
+    id :<%= test_suite_id %>
+    title '<%= title_name %> Test Suite'
+    description '<%= human_name %> test suite.'
+
+    # These inputs will be available to all tests in this suite
+    input :url,
+          title: 'FHIR Server Base Url'
+
+    input :credentials,
+          title: 'OAuth Credentials',
+          type: :oauth_credentials,
+          optional: true
+
+    # All FHIR requests in this suite will use this FHIR client
+    fhir_client do
+      url :url
+      oauth_credentials :credentials
+    end
+
+    # All FHIR validation requests will use this FHIR validator
+    fhir_resource_validator do
+      # igs 'identifier#version' # Use this method for published IGs/versions
+      # igs 'igs/filename.tgz'   # Use this otherwise
+
+      exclude_message do |message|
+        message.message.match?(/\A\S+: \S+: URL value '.*' does not resolve/)
+      end
+    end
+
+    # Tests and TestGroups can be defined inline
+    group do
+      id :capability_statement
+      title 'Capability Statement'
+      description 'Verify that the server has a CapabilityStatement'
+
+      test do
+        id :capability_statement_read
+        title 'Read CapabilityStatement'
+        description 'Read CapabilityStatement from /metadata endpoint'
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+        end
+      end
+    end
+
+    # Tests and TestGroups can be written in separate files and then included
+    # using their id
+    group from: :patient_group
+  end
+end

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

@@ -0,0 +1,3 @@
+module <%= module_name %>
+  VERSION = '0.0.0'.freeze
+end

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

@@ -1,58 +1 @@
-require_relative '<%= library_name %>/patient_group'
-
-module <%= module_name %>
-  class Suite < Inferno::TestSuite
-    id :<%= test_suite_id %>
-    title '<%= title_name %> Test Suite'
-    description '<%= human_name %> test suite.'
-
-    # These inputs will be available to all tests in this suite
-    input :url,
-          title: 'FHIR Server Base Url'
-
-    input :credentials,
-          title: 'OAuth Credentials',
-          type: :oauth_credentials,
-          optional: true
-
-    # All FHIR requests in this suite will use this FHIR client
-    fhir_client do
-      url :url
-      oauth_credentials :credentials
-    end
-
-    # All FHIR validation requests will use this FHIR validator
-    fhir_resource_validator do
-      # igs 'identifier#version' # Use this method for published IGs/versions
-      # igs 'igs/filename.tgz'   # Use this otherwise
-
-      exclude_message do |message|
-        message.message.match?(/\A\S+: \S+: URL value '.*' does not resolve/)
-      end
-    end
-
-    # Tests and TestGroups can be defined inline
-    group do
-      id :capability_statement
-      title 'Capability Statement'
-      description 'Verify that the server has a CapabilityStatement'
-
-      test do
-        id :capability_statement_read
-        title 'Read CapabilityStatement'
-        description 'Read CapabilityStatement from /metadata endpoint'
-
-        run do
-          fhir_get_capability_statement
-
-          assert_response_status(200)
-          assert_resource_type(:capability_statement)
-        end
-      end
-    end
-
-    # Tests and TestGroups can be written in separate files and then included
-    # using their id
-    group from: :patient_group
-  end
-end
+require_relative '<%= library_name %>/suite'

data/lib/inferno/apps/web/application.rb

@@ -1,6 +1,10 @@
 require 'hanami/middleware/body_parser'
 require_relative 'router'
 
+# Only required to monkey patch the JSON parser to support application/fhir+json
+require 'hanami/middleware/body_parser/json_parser'
+require_relative '../../ext/json_parser'
+
 module Inferno
   module Web
     def self.app

data/lib/inferno/apps/web/index.html.erb

@@ -9,10 +9,18 @@
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="theme-color" content="#000000" />
     <meta id="base-path" name="base-path" content="<%= Inferno::Application['base_path'] %>">
-    <meta
-      name="description"
-      content="FHIR Testing"
-    />
+    
+    <!-- Social media link unfurling meta tags -->
+    <title>Inferno Test Session</title>
+    <link rel="canonical" href="<%= Inferno::Application['base_url'] %>" />
+    <meta name="application-name" content="Inferno" />
+    <meta name="og:image" content="<%= Inferno::Application['inferno_host'] %><%= Inferno::Application['public_path'] %>/logo192.png" />
+    <meta name="og:type" content="website" />
+    <meta name="og:url" content="<%= Inferno::Application['base_url'] %>" />
+    <meta name="og:site_name" content="Inferno" />
+    <meta name="twitter:card" content="summary" />
+    <meta name="twitter:image" content="<%= Inferno::Application['inferno_host'] %><%= Inferno::Application['public_path'] %>/logo192.png" />
+    
     <link rel="apple-touch-icon" href="<%= Inferno::Application['public_path'] %>/logo192.png" />
     <!--
       manifest.json provides metadata used when your web app is installed on a

data/lib/inferno/apps/web/serializers/input.rb

@@ -1,3 +1,4 @@
+require_relative 'markdown_extractor'
 require_relative 'serializer'
 
 module Inferno
@@ -7,7 +8,7 @@ module Inferno
         identifier :name
 
         field :title, if: :field_present?
-        field :description, if: :field_present?
+        field :description, extractor: MarkdownExtractor, if: :field_present?
         field :type, if: :field_present?
         field :default, if: :field_present?
         field :optional, if: :field_present?

data/lib/inferno/apps/web/serializers/markdown_extractor.rb

@@ -0,0 +1,16 @@
+require 'blueprinter'
+require_relative '../../../utils/markdown_formatter'
+
+module Inferno
+  module Web
+    module Serializers
+      class MarkdownExtractor < Blueprinter::Extractor
+        include Inferno::Utils::MarkdownFormatter
+
+        def extract(field_name, object, _local_options, _options = {})
+          format_markdown(object.send(field_name))
+        end
+      end
+    end
+  end
+end

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

@@ -10,5 +10,6 @@ Inferno::Application.register_provider(:executor) do
     end
 
     target_container.start :suites
+    target_container.start :presets
   end
 end

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

@@ -4,9 +4,26 @@ Inferno::Application.register_provider(:presets) do
   prepare do
     target_container.start :suites
 
+    presets_repo = Inferno::Repositories::Presets.new
+
+    test_kit_gems =
+      Bundler
+        .definition
+        .specs
+        .select { |spec| spec.metadata.fetch('inferno_test_kit', 'false').casecmp? 'true' }
+
     files_to_load = Dir.glob(['config/presets/*.json', 'config/presets/*.json.erb'])
+    files_to_load +=
+      test_kit_gems.flat_map do |gem|
+        [
+          Dir.glob([File.join(gem.full_gem_path, 'config', 'presets', '*.json')]),
+          Dir.glob([File.join(gem.full_gem_path, 'config', 'presets', '*.json.erb')])
+        ].flatten
+      end
+
+    files_to_load.compact!
+    files_to_load.uniq!
     files_to_load.map! { |path| File.realpath(path) }
-    presets_repo = Inferno::Repositories::Presets.new
 
     files_to_load.each do |path|
       presets_repo.insert_from_file(path)

data/lib/inferno/dsl/fhir_evaluation/config.rb

@@ -0,0 +1,21 @@
+module Inferno
+  module DSL
+    module FHIREvaluation
+      class Config
+        DEFAULT_FILE = File.join(__dir__, 'default.yml')
+        attr_accessor :data
+
+        # To-do: add config_file as arguments
+        def initialize(config_file = nil)
+          @data = if config_file.nil?
+                    YAML.load_file(File.absolute_path(DEFAULT_FILE))
+                  else
+                    YAML.load_file(File.absolute_path(config_file))
+                  end
+
+          raise(TypeError, 'Malformed configuration') unless @data.is_a?(Hash)
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/dataset_loader.rb

@@ -0,0 +1,33 @@
+module Inferno
+  module DSL
+    module FHIREvaluation
+      module DatasetLoader
+        def self.from_contents(source_array)
+          dataset = []
+
+          source_array.each do |json|
+            resource = FHIR::Json.from_json(json)
+            next if resource.nil?
+
+            dataset.push resource
+          end
+
+          dataset
+        end
+
+        def self.from_path(path)
+          dataset = []
+
+          Dir["#{path}/*.json"].each do |f|
+            resource = FHIR::Json.from_json(File.read(f))
+            next if resource.nil?
+
+            dataset.push resource
+          end
+
+          dataset
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/evaluation_context.rb

@@ -0,0 +1,25 @@
+module Inferno
+  module DSL
+    module FHIREvaluation
+      # EvaluationContext is a wrapper class around the concepts needed to perform an evaluation:
+      # - The IG used as the basis for evaluation
+      # - The data being evaluated
+      # - A summary/characterization of the data
+      # - Evaluation results
+      class EvaluationContext
+        attr_reader :ig, :data, :results, :config
+
+        def initialize(ig, data, config) # rubocop:disable Naming/MethodParameterName
+          @ig = ig
+          @data = data
+          @results = []
+          @config = config
+        end
+
+        def add_result(result)
+          results.push result
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/evaluation_result.rb

@@ -0,0 +1,62 @@
+module Inferno
+  module DSL
+    module FHIREvaluation
+      # The result of a Rule evaluating a data set.
+      class EvaluationResult
+        attr_accessor :message,
+                      :severity,   # fatal | error | warning | information | success
+                      :issue_type, # https://www.hl7.org/fhir/valueset-issue-type.html
+                      :threshold,  # quantitative value that a rule checks for
+                      :value,      # actual observed value
+                      :rule        # Rule that produced this result
+
+        def initialize(message, severity: 'warning', issue_type: 'business-rule', threshold: nil, value: nil, rule: nil)
+          @message = message
+          @severity = severity
+          @issue_type = issue_type
+          @threshold = threshold
+          @value = value
+          @rule = rule
+        end
+
+        def to_s
+          "#{severity.upcase}: #{message}"
+        end
+
+        def to_oo_issue
+          issue = {
+            severity:,
+            code: issue_type,
+            details: { text: message }
+          }
+
+          if threshold
+            issue[:extension] ||= []
+            issue[:extension].push({
+                                     # TODO: pick real extension for this
+                                     url: 'https://inferno-framework.github.io/fhir_evaluator/StructureDefinition/operationoutcome-issue-threshold',
+                                     valueDecimal: threshold
+                                   })
+          end
+
+          if value
+            issue[:extension] ||= []
+            issue[:extension].push({
+                                     # TODO: pick real extension for this
+                                     url: 'https://inferno-framework.github.io/fhir_evaluator/StructureDefinition/operationoutcome-issue-value',
+                                     valueDecimal: value
+                                   })
+          end
+
+          issue
+        end
+
+        def self.to_operation_outcome(results)
+          FHIR::OperationOutcome.new({
+                                       issue: results.map(&:to_oo_issue)
+                                     })
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/evaluator.rb

@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+require_relative 'config'
+require_relative 'rule'
+require_relative 'evaluation_context'
+require_relative 'evaluation_result'
+require_relative 'dataset_loader'
+
+module Inferno
+  module DSL
+    module FHIREvaluation
+      class Evaluator
+        attr_accessor :ig
+
+        def initialize(ig) # rubocop:disable Naming/MethodParameterName
+          @ig = ig
+        end
+
+        def evaluate(data, config = Config.new)
+          context = EvaluationContext.new(@ig, data, config)
+
+          active_rules = []
+          config.data['Rule'].each do |rulename, rule_details|
+            active_rules << rulename if rule_details['Enabled']
+          end
+
+          Rule.descendants.each do |rule|
+            rule.new.check(context) if active_rules.include?(rule.name.demodulize)
+          end
+
+          context.results
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/rule.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Inferno
+  module DSL
+    module FHIREvaluation
+      class Rule
+        def check(_context)
+          raise 'not implemented'
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/suite_endpoint.rb

@@ -9,54 +9,54 @@ module Inferno
     # endpoint](https://github.com/hanami/controller/tree/v2.0.0).
     #
     # @example
-    # class AuthorizedEndpoint < Inferno::DSL::SuiteEndpoint
-    #   # Identify the incoming request based on a bearer token
-    #   def test_run_identifier
-    #     request.header['authorization']&.delete_prefix('Bearer ')
-    #   end
+    #     class AuthorizedEndpoint < Inferno::DSL::SuiteEndpoint
+    #       # Identify the incoming request based on a bearer token
+    #       def test_run_identifier
+    #         request.header['authorization']&.delete_prefix('Bearer ')
+    #       end
     #
-    #   # Return a json FHIR Patient resource
-    #   def make_response
-    #     response.status = 200
-    #     response.body = FHIR::Patient.new(id: 'abcdef').to_json
-    #     response.format = :json
-    #   end
+    #       # Return a json FHIR Patient resource
+    #       def make_response
+    #         response.status = 200
+    #         response.body = FHIR::Patient.new(id: 'abcdef').to_json
+    #         response.format = :json
+    #       end
     #
-    #   # Update the waiting test to pass when the incoming request is received.
-    #   # This will resume the test run.
-    #   def update_result
-    #     results_repo.update(result.id, result: 'pass')
-    #   end
+    #       # Update the waiting test to pass when the incoming request is received.
+    #       # This will resume the test run.
+    #       def update_result
+    #         results_repo.update(result.id, result: 'pass')
+    #       end
     #
-    #   # Apply the 'authorized' tag to the incoming request so that it may be
-    #   # used by later tests.
-    #   def tags
-    #     ['authorized']
-    #   end
-    # end
+    #       # Apply the 'authorized' tag to the incoming request so that it may be
+    #       # used by later tests.
+    #       def tags
+    #         ['authorized']
+    #       end
+    #     end
     #
-    # class AuthorizedRequestSuite < Inferno::TestSuite
-    #   id :authorized_suite
-    #   suite_endpoint :get, '/authorized_endpoint', AuthorizedEndpoint
+    #     class AuthorizedRequestSuite < Inferno::TestSuite
+    #       id :authorized_suite
+    #       suite_endpoint :get, '/authorized_endpoint', AuthorizedEndpoint
     #
-    #   group do
-    #     title 'Authorized Request Group'
+    #       group do
+    #         title 'Authorized Request Group'
     #
-    #     test do
-    #       title 'Wait for authorized request'
+    #         test do
+    #           title 'Wait for authorized request'
     #
-    #       input :bearer_token
+    #           input :bearer_token
     #
-    #       run do
-    #         wait(
-    #           identifier: bearer_token,
-    #           message: "Waiting to receive a request with bearer_token: #{bearer_token}" \
-    #                    "at `#{Inferno::Application['base_url']}/custom/authorized_suite/authorized_endpoint`"
-    #         )
+    #           run do
+    #             wait(
+    #               identifier: bearer_token,
+    #               message: "Waiting to receive a request with bearer_token: #{bearer_token}" \
+    #                        "at `#{Inferno::Application['base_url']}/custom/authorized_suite/authorized_endpoint`"
+    #             )
+    #           end
+    #         end
     #       end
     #     end
-    #   end
-    # end
     class SuiteEndpoint < Hanami::Action
       attr_reader :req, :res
 
@@ -69,11 +69,11 @@ module Inferno
       # @return [String]
       #
       # @example
-      # def test_run_identifier
-      #   # Identify the test session of an incoming request based on the bearer
-      #   # token
-      #   request.headers['authorization']&.delete_prefix('Bearer ')
-      # end
+      #   def test_run_identifier
+      #     # Identify the test session of an incoming request based on the bearer
+      #     # token
+      #     request.headers['authorization']&.delete_prefix('Bearer ')
+      #   end
       def test_run_identifier
         nil
       end
@@ -83,11 +83,11 @@ module Inferno
       # @return [Void]
       #
       # @example
-      # def make_response
-      #   response.status = 200
-      #   response.body = { abc: 123 }.to_json
-      #   response.format = :json
-      # end
+      #   def make_response
+      #     response.status = 200
+      #     response.body = { abc: 123 }.to_json
+      #     response.format = :json
+      #   end
       def make_response
         nil
       end
@@ -113,9 +113,9 @@ module Inferno
       # @return [Void]
       #
       # @example
-      # def update_result
-      #   results_repo.update(result.id, result: 'pass')
-      # end
+      #   def update_result
+      #     results_repo.update(result.id, result: 'pass')
+      #   end
       def update_result
         nil
       end
@@ -165,9 +165,9 @@ module Inferno
       # @return [Hanami::Action::Request]
       #
       # @example
-      # request.params               # Get url/query params
-      # request.body.read            # Get body
-      # request.headers['accept']    # Get Accept header
+      #   request.params               # Get url/query params
+      #   request.body.read            # Get body
+      #   request.headers['accept']    # Get Accept header
       def request
         req
       end
@@ -178,10 +178,10 @@ module Inferno
       # @return [Hanami::Action::Response]
       #
       # @example
-      # response.status = 200        # Set the status
-      # response.body = 'Ok'         # Set the body
-      # # Set headers
-      # response.headers.merge!('X-Custom-Header' => 'CUSTOM_HEADER_VALUE')
+      #   response.status = 200        # Set the status
+      #   response.body = 'Ok'         # Set the body
+      #   # Set headers
+      #   response.headers.merge!('X-Custom-Header' => 'CUSTOM_HEADER_VALUE')
       def response
         res
       end

data/lib/inferno/dsl.rb

@@ -1,6 +1,7 @@
 require_relative 'dsl/assertions'
 require_relative 'dsl/fhir_client'
 require_relative 'dsl/fhir_validation'
+require_relative 'dsl/fhir_evaluation/evaluator'
 require_relative 'dsl/fhir_resource_validation'
 require_relative 'dsl/fhirpath_evaluation'
 require_relative 'dsl/http_client'
@@ -18,6 +19,7 @@ module Inferno
       HTTPClient,
       Results,
       FHIRValidation,
+      FHIREvaluation,
       FHIRResourceValidation,
       FhirpathEvaluation,
       Messages

data/lib/inferno/entities/test_kit.rb

@@ -6,7 +6,7 @@ module Inferno
     # @example
     #
     #   module USCoreTestKit
-    #     class TestKit < Inferno::Entities::TestKit
+    #     class Metadata < Inferno::Entities::TestKit
     #       id :us_core
     #       title 'US Core Test Kit'
     #       description <<~DESCRIPTION
@@ -156,7 +156,7 @@ module Inferno
 
         # @private
         def repository
-          @repository ||= Inferno::Repositories::TestKits
+          @repository ||= Inferno::Repositories::TestKits.new
         end
 
         # @private
@@ -168,4 +168,6 @@ module Inferno
       end
     end
   end
+
+  TestKit = Entities::TestKit
 end

data/lib/inferno/entities/test_suite.rb

@@ -84,15 +84,16 @@ module Inferno
           }
         end
 
-        # Set/get the version of this test suite.
+        # Set/get the version of this test suite. Defaults to the TestKit
+        # version.
         #
         # @param version [String]
         #
         # @return [String, nil]
         def version(version = nil)
-          return @version if version.nil?
+          @version = version if version.present?
 
-          @version = version
+          @version || test_kit&.version
         end
 
         # @private
@@ -186,6 +187,25 @@ module Inferno
 
           @suite_summary = format_markdown(suite_summary)
         end
+
+        # Get the TestKit this suite belongs to
+        #
+        # @return [Inferno::Entities::TestKit]
+        def test_kit
+          return @test_kit if @test_kit
+
+          module_name = name
+
+          while module_name.present? && @test_kit.nil?
+            module_name = module_name.deconstantize
+
+            next unless const_defined?("#{module_name}::Metadata")
+
+            @test_kit = const_get("#{module_name}::Metadata")
+          end
+
+          @test_kit
+        end
       end
     end
   end

data/lib/inferno/entities.rb

@@ -8,6 +8,7 @@ require_relative 'entities/result'
 require_relative 'entities/session_data'
 require_relative 'entities/test'
 require_relative 'entities/test_group'
+require_relative 'entities/test_kit'
 require_relative 'entities/test_run'
 require_relative 'entities/test_session'
 require_relative 'entities/test_suite'

data/lib/inferno/ext/json_parser.rb

@@ -0,0 +1,11 @@
+module Hanami
+  module Middleware
+    class BodyParser
+      class JsonParser
+        def self.mime_types
+          ['application/json', 'application/vnd.api+json', 'application/fhir+json']
+        end
+      end
+    end
+  end
+end

data/lib/inferno/repositories/presets.rb

@@ -8,14 +8,20 @@ module Inferno
     # Repository that deals with persistence for the `Preset` entity.
     class Presets < InMemoryRepository
       def insert_from_file(path)
-        case path
-        when /\.json$/
-          preset_hash = JSON.parse(File.read(path))
-        when /\.erb$/
-          templated = ERB.new(File.read(path)).result
-          preset_hash = JSON.parse(templated)
+        raw_contents =
+          case path
+          when /\.json$/
+            File.read(path)
+          when /\.erb$/
+            ERB.new(File.read(path)).result
+          end
+
+        if Application['base_url'].start_with? 'https://inferno-qa.healthit.gov'
+          raw_contents.gsub!('https://inferno.healthit.gov', 'https://inferno-qa.healthit.gov')
         end
 
+        preset_hash = JSON.parse(raw_contents)
+
         preset_hash.deep_symbolize_keys!
         preset_hash[:id] ||= SecureRandom.uuid
         preset = Entities::Preset.new(preset_hash)

data/lib/inferno/result_summarizer.rb

@@ -12,6 +12,8 @@ module Inferno
     end
 
     def summarize
+      return 'wait' if results.any? { |result| result.result == 'wait' }
+
       return 'pass' if optional_results_passing_criteria_met?
 
       prioritized_result_strings.find { |result_string| unique_result_strings.include? result_string }

data/lib/inferno/utils/named_thor_actions.rb

@@ -25,8 +25,12 @@ module Inferno
         human_name.split.map(&:capitalize).join(' ')
       end
 
+      def test_kit_id
+        library_name.delete_suffix('_test_kit')
+      end
+
       def test_suite_id
-        "#{library_name}_test_suite"
+        test_kit_id
       end
     end
   end

data/lib/inferno/version.rb

@@ -1,4 +1,4 @@
 module Inferno
   # Standard patterns for gem versions: https://guides.rubygems.org/patterns/
-  VERSION = '0.5.1'.freeze
+  VERSION = '0.5.3'.freeze
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: inferno_core
 version: !ruby/object:Gem::Version
-  version: 0.5.1
+  version: 0.5.3
 platform: ruby
 authors:
 - Stephen MacVicar
@@ -10,7 +10,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-11-26 00:00:00.000000000 Z
+date: 2024-12-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -390,6 +390,7 @@ files:
 - lib/inferno.rb
 - lib/inferno/apps/cli.rb
 - lib/inferno/apps/cli/console.rb
+- lib/inferno/apps/cli/evaluate.rb
 - lib/inferno/apps/cli/execute.rb
 - lib/inferno/apps/cli/execute/console_outputter.rb
 - lib/inferno/apps/cli/execute/json_outputter.rb
@@ -432,7 +433,10 @@ files:
 - lib/inferno/apps/cli/templates/lib/%library_name%/igs/.keep
 - lib/inferno/apps/cli/templates/lib/%library_name%/igs/README.md
 - lib/inferno/apps/cli/templates/lib/%library_name%/igs/put_ig_package_dot_tgz_here
+- lib/inferno/apps/cli/templates/lib/%library_name%/metadata.rb.tt
 - lib/inferno/apps/cli/templates/lib/%library_name%/patient_group.rb.tt
+- lib/inferno/apps/cli/templates/lib/%library_name%/suite.rb.tt
+- lib/inferno/apps/cli/templates/lib/%library_name%/version.rb.tt
 - lib/inferno/apps/cli/templates/run.sh
 - lib/inferno/apps/cli/templates/setup.sh
 - lib/inferno/apps/cli/templates/spec/%library_name%/patient_group_spec.rb.tt
@@ -461,6 +465,7 @@ files:
 - lib/inferno/apps/web/serializers/hash_value_extractor.rb
 - lib/inferno/apps/web/serializers/header.rb
 - lib/inferno/apps/web/serializers/input.rb
+- lib/inferno/apps/web/serializers/markdown_extractor.rb
 - lib/inferno/apps/web/serializers/message.rb
 - lib/inferno/apps/web/serializers/preset.rb
 - lib/inferno/apps/web/serializers/request.rb
@@ -500,6 +505,12 @@ files:
 - lib/inferno/dsl/configurable.rb
 - lib/inferno/dsl/fhir_client.rb
 - lib/inferno/dsl/fhir_client_builder.rb
+- lib/inferno/dsl/fhir_evaluation/config.rb
+- lib/inferno/dsl/fhir_evaluation/dataset_loader.rb
+- lib/inferno/dsl/fhir_evaluation/evaluation_context.rb
+- lib/inferno/dsl/fhir_evaluation/evaluation_result.rb
+- lib/inferno/dsl/fhir_evaluation/evaluator.rb
+- lib/inferno/dsl/fhir_evaluation/rule.rb
 - lib/inferno/dsl/fhir_resource_validation.rb
 - lib/inferno/dsl/fhir_validation.rb
 - lib/inferno/dsl/fhirpath_evaluation.rb
@@ -539,6 +550,7 @@ files:
 - lib/inferno/exceptions.rb
 - lib/inferno/ext/fhir_client.rb
 - lib/inferno/ext/fhir_models.rb
+- lib/inferno/ext/json_parser.rb
 - lib/inferno/ext/rack.rb
 - lib/inferno/jobs.rb
 - lib/inferno/jobs/execute_test_run.rb