inferno_core 0.6.6 → 0.6.8

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 61f9b65616cf01dd42c838ab0b9be5c38490dea22bb2a3481a82c30a25c687e2aada97321498920f6219a62afe88445ad95e71b2300859fce5ed19af7cef1f78

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

@@ -1,6 +1,6 @@
-require_relative '../../../inferno/dsl/fhir_evaluation/evaluator'
-require_relative '../../../inferno/dsl/fhir_evaluation/config'
-require_relative '../../../inferno/entities'
+require_relative '../../dsl/fhir_evaluation/evaluator'
+require_relative '../../dsl/fhir_evaluation/config'
+require_relative '../../entities'
 require_relative '../../utils/ig_downloader'
 
 require 'tempfile'
@@ -9,6 +9,12 @@ module Inferno
   module CLI
     class Evaluate < Thor::Group
       def evaluate(ig_path, data_path, _log_level)
+        # NOTE: repositories is required here rather than at the top of the file because
+        # the tree of requires means that this file and its requires get required by every CLI app.
+        # Sequel::Model, used in some repositories, fetches the table schema at instantiation.
+        # This breaks the `migrate` task by fetching a table before the task runs/creates it.
+        require_relative '../../repositories'
+
         validate_args(ig_path, data_path)
         ig = Inferno::Repositories::IGs.new.find_or_load(ig_path)
 
@@ -21,7 +27,9 @@ module Inferno
             ig.examples
           end
 
-        evaluator = Inferno::DSL::FHIREvaluation::Evaluator.new(ig)
+        validator = setup_validator(ig_path)
+
+        evaluator = Inferno::DSL::FHIREvaluation::Evaluator.new(ig, validator)
 
         config = Inferno::DSL::FHIREvaluation::Config.new
         results = evaluator.evaluate(data, config)
@@ -44,6 +52,24 @@ module Inferno
         puts '**WARNING** The selected IG targets a FHIR version higher than 4.0.1, which is not supported by Inferno.'
       end
 
+      def setup_validator(ig_path)
+        igs_directory = File.join(Dir.pwd, 'data', 'igs')
+        if File.exist?(ig_path) && !File.realpath(ig_path).start_with?(igs_directory)
+          puts "Copying #{File.basename(ig_path)} to data/igs so it is accessible to validator"
+          destination_file_path = File.join(igs_directory, File.basename(ig_path))
+          FileUtils.copy_file(ig_path, destination_file_path, true)
+          ig_path = "igs/#{File.basename(ig_path)}"
+        end
+        Inferno::DSL::FHIRResourceValidation::Validator.new(:default, 'evaluator_cli') do
+          igs(ig_path)
+
+          cli_context do
+            # For our purposes, code display mismatches should be warnings and not affect profile conformance
+            displayWarnings(true)
+          end
+        end
+      end
+
       def output_results(results, output)
         if output&.end_with?('json')
           oo = FhirEvaluator::EvaluationResult.to_operation_outcome(results)

data/lib/inferno/dsl/auth_info.rb

@@ -132,7 +132,7 @@ module Inferno
       # @!attribute [rw] name
 
       # @private
-      def initialize(raw_attributes_hash)
+      def initialize(raw_attributes_hash) # rubocop:disable Metrics/CyclomaticComplexity
         attributes_hash = raw_attributes_hash.symbolize_keys
 
         invalid_keys = attributes_hash.keys - ATTRIBUTES
@@ -143,6 +143,8 @@ module Inferno
           value = DateTime.parse(value) if name == :issue_time && value.is_a?(String)
 
           instance_variable_set(:"@#{name}", value)
+        rescue Date::Error
+          Inferno::Application['logger'].error("Received invalid date: #{value.inspect}")
         end
 
         self.issue_time = DateTime.now if access_token.present? && issue_time.blank?

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

@@ -55,10 +55,16 @@ module Inferno
           declared_profiles.include?(profile_url) || declared_profiles.include?(versioned_url)
         end
 
-        # @private until implemented
-        def validates_profile?(_resource, _profile, _validator)
-          raise 'Profile validation is not yet implemented. ' \
-                'Set considerValidationResults=false.'
+        # Check if the given resource validates against the given profile.
+        # "Validates" means the provided Validator instance returns no fatal or error messages.
+        # @param resource [FHIR::Resource]
+        # @param profile [FHIR::StructureDefinition]
+        # @param validator [Inferno::DSL::FHIRResourceValidation::Validator]
+        def validates_profile?(resource, profile, validator)
+          return false if validator.nil?
+
+          runnable = Inferno::Entities::Test.new
+          validator.resource_is_valid?(resource, profile.url, runnable, add_messages_to_runnable: false)
         end
       end
     end

data/lib/inferno/dsl/fhir_evaluation/rules/all_defined_extensions_have_examples.rb

@@ -0,0 +1,58 @@
+# frozen_string_literal: true
+
+module Inferno
+  module DSL
+    module FHIREvaluation
+      module Rules
+        class AllDefinedExtensionsHaveExamples < Rule
+          attr_accessor :used_extensions, :unused_extensions
+
+          def check(context)
+            @used_extensions = context.data.map { |e| extension_urls(e) }.flatten.uniq
+            @unused_extensions = []
+
+            get_unused_extensions(context.ig.extensions) do |extension|
+              next true if extension.context.any? do |ctx|
+                # Skip extensions that are defined for definitional artifacts.
+                # For example, US Core's uscdi-requirement extension is applied to
+                # the profiles and extensions of the IG, not data that conforms to the IG.
+                # There may eventually be cases where SD/ED are data, so this may become configurable.
+                ctx.expression == 'StructureDefinition' || ctx.expression == 'ElementDefinition'
+              end
+
+              versioned_url = "#{extension.url}|#{extension.version}"
+              used_extensions.include?(extension.url) || used_extensions.include?(versioned_url)
+            end
+
+            if unused_extensions.any?
+              message = "Found unused extensions defined in the IG: \n\t #{unused_extensions.join(', ')}"
+              result = EvaluationResult.new(message, rule: self)
+            else
+              message = 'All defined extensions are represented in examples'
+              result = EvaluationResult.new(message, severity: 'success', rule: self)
+            end
+
+            context.add_result result
+          end
+
+          def extension_urls(resource)
+            urls = []
+            resource.each_element do |value, _metadata, path|
+              path_elements = path.split('.')
+              next unless path_elements.length > 1
+
+              urls << value if path_elements[-2].include?('extension') && path_elements[-1] == 'url'
+            end
+            urls.uniq
+          end
+
+          def get_unused_extensions(extensions, &extension_filter)
+            extensions.each do |extension|
+              unused_extensions.push extension.url unless extension_filter.call(extension)
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/rules/all_profiles_have_examples.rb

@@ -0,0 +1,49 @@
+module Inferno
+  module DSL
+    module FHIREvaluation
+      module Rules
+        class AllProfilesHaveExamples < Rule
+          include ProfileConformanceHelper
+
+          attr_accessor :context, :unused_profile_urls, :all_resources
+
+          def check(context)
+            @context = context
+            @unused_profile_urls = []
+            @all_resources = []
+            options = context.config.data['Rule']['AllProfilesHaveExamples']['ConformanceOptions'].to_options
+
+            context.data.map { |entry| extract_resources(entry) }
+            all_resources.uniq!
+
+            context.ig.profiles.each do |profile|
+              profile_used = all_resources.any? do |resource|
+                conforms_to_profile?(resource, profile, options, context.validator)
+              end
+              unused_profile_urls << profile.url unless profile_used
+            end
+
+            unused_profile_urls.uniq!
+
+            if unused_profile_urls.any?
+              message = "Found profiles without examples: \n\t #{unused_profile_urls.join(', ')}"
+              result = EvaluationResult.new(message, rule: self)
+            else
+              message = 'All profiles have example instances.'
+              result = EvaluationResult.new(message, severity: 'success', rule: self)
+            end
+
+            context.add_result result
+          end
+
+          def extract_resources(resource)
+            all_resources << resource
+            return unless resource.resourceType == 'Bundle'
+
+            resource.entry.map { |entry| extract_resources(entry.resource) }.flatten
+          end
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/rules/all_search_parameters_have_examples.rb

@@ -0,0 +1,79 @@
+require_relative '../../fhirpath_evaluation'
+
+module Inferno
+  module DSL
+    module FHIREvaluation
+      module Rules
+        class AllSearchParametersHaveExamples < Rule
+          include FhirpathEvaluation
+
+          def check(context)
+            unless ENV['FHIRPATH_URL']
+              message = 'FHIRPATH_URL is not found. Skipping rule AllSearchParametersHaveExamples.'
+              result = EvaluationResult.new(message, severity: 'warning', rule: self)
+              context.add_result result
+              return
+            end
+
+            unused_resource_urls = []
+            search_params = context.ig.resources_by_type['SearchParameter']
+
+            search_params.each do |search_param|
+              unused_resource_urls.push search_param.url unless param_is_used?(search_param, context)
+            end
+
+            if unused_resource_urls.any?
+              message = "Found SearchParameters with no searchable data: \n\t#{unused_resource_urls.join(' ,')}"
+              result = EvaluationResult.new(message, rule: self)
+            elsif !search_params.empty?
+              message = 'All SearchParameters have examples'
+              result = EvaluationResult.new(message, severity: 'success', rule: self)
+            else
+              message = 'IG contains no SearchParameter'
+              result = EvaluationResult.new(message, severity: 'information', rule: self)
+            end
+
+            context.add_result result
+          end
+
+          def param_is_used?(param, context)
+            # Assume that all params have an expression (fhirpath)
+            # This is not guaranteed since the field is 0..1
+            # but without it there's no other way to select a value
+            # Return warning if params don't include expression
+            unless param.expression
+              message = "Search parameter #{param.url} doesn't have an expression."
+              result = EvaluationResult.new(message, severity: 'warning', rule: self)
+              context.add_result result
+              return false
+            end
+
+            used = false
+
+            context.data.each do |resource|
+              next unless param.base.include? resource.resourceType
+
+              begin
+                result = evaluate_fhirpath(resource: resource, path: param.expression)
+              rescue StandardError => e
+                message = "SearchParameter #{param.url} failed to evaluate due to an error. " \
+                          "Expression: #{param.expression}. #{e}"
+                result = EvaluationResult.new(message)
+                context.add_result result
+
+                used = true
+                break
+              end
+
+              if result.present?
+                used = true
+                break
+              end
+            end
+            used
+          end
+        end
+      end
+    end
+  end
+end