inferno_core 0.5.2 → 0.5.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 41fdda8d351bb039a654949835c70ed19999cbce0ccba735b4154774cdc61225
-  data.tar.gz: 1c0a86692b2a231af565fd6695fcc229d0ea51c2acf55e4236a5ff551e0a83a9
+  metadata.gz: e11d6b274778016418f7189d8ec9e724cf20861c6e03385dc9c302299f198d18
+  data.tar.gz: '09c65484d51b2f7be0a3985b374d51593d59c432ba11c21bd10d54c798ccafa4'
 SHA512:
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-  data.tar.gz: 6dd48102d0ba87b339f5534312a949f390b69ad26741e2be73db1ec287b281efa9842c814ca6e8a4250745597909111b10759b2d171711686025c060194dad61
+  metadata.gz: 0daf93ce97d8a5a8e9b409200d7c001e4ac49107887db05073399a74795a94b449d3c1eb1d139214c1402e1ea10a954ee1271b80c642909c379cd7bb0ba7a1f0
+  data.tar.gz: 3a70bb18128af1494e0fcd1a023d8e18e8043dd535ae9c00f8471c8eb85e23678fa7c8bcb19591852c3593c6588ba92af206a90644cf6288659179fef98c1a41

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

@@ -0,0 +1,97 @@
+require_relative '../../../inferno/dsl/fhir_evaluation/evaluator'
+require_relative '../../../inferno/entities'
+require_relative '../../utils/ig_downloader'
+
+require 'tempfile'
+
+module Inferno
+  module CLI
+    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)
+
+        # Rule execution, and result output below will be integrated soon.
+
+        # 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 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)
+          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/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.evaluate(ig_path, options[:data_path], Logger::INFO)
+      end
+
       desc 'console', 'Start an interactive console session with Inferno'
       def console
         Migration.new.run(Logger::INFO)

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/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/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