inferno_core 0.6.7 → 0.6.8

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/inferno/apps/cli/evaluate.rb

@@ -1,7 +1,6 @@
 require_relative '../../dsl/fhir_evaluation/evaluator'
 require_relative '../../dsl/fhir_evaluation/config'
 require_relative '../../entities'
-require_relative '../../repositories'
 require_relative '../../utils/ig_downloader'
 
 require 'tempfile'
@@ -10,6 +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)
 

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