inferno_core 0.6.14 → 0.6.16

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: ab5cb618341fec45b35d55349a9138c9a544d37327fd8bd971dbb9c8c6049e15
+  metadata.gz: bdded0041b27a81a8cedae003b073e738a719eda6671cb39b1556bd165a986c9
+  data.tar.gz: f9cb54ff76488ce34f8f9c9464bbc3588f67f3931d6eef284a78d1af32a0b78e
 SHA512:
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-  data.tar.gz: d9b9973007a9f1e2f1064945456ac0b2fbfe94359d33c3b84119bfe7b391c08b2d085d22cf9823ce61466d249cdea0f552b4caee6fb37cf56650bd190f324341
+  metadata.gz: e53518c76be16a5cc631a503c84388b706d2030a30469048379f3b4d91d1525d5e1ee373cb454c191b97eb857c9682d821270c9c2a35cfe408b5fd7fa405a236
+  data.tar.gz: a078da89879d42f3cda28ebc8dca66feca2a85e9f735868bbcd4dbf70774ef268e613fd4aad4fe076002af1d3d7035bd02de8c2679d2ce17b8ee05a794f629ab

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

@@ -112,7 +112,7 @@ module Inferno
         Inferno::DSL::FHIRResourceValidation::Validator.new(:default, 'evaluator_cli') do
           igs(ig_path)
 
-          cli_context do
+          validation_context do
             # For our purposes, code display mismatches should be warnings and not affect profile conformance
             displayWarnings(true)
           end

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

@@ -12,6 +12,9 @@ module Inferno
       LONGDESC
       def export_csv
         ENV['NO_DB'] = 'true'
+
+        require_relative '../../../inferno'
+
         RequirementsExporter.new.run
       end
 
@@ -22,6 +25,11 @@ module Inferno
       LONGDESC
       def check
         ENV['NO_DB'] = 'true'
+
+        require_relative '../../../inferno'
+
+        Inferno::Application.start(:requirements)
+
         RequirementsExporter.new.run_check
       end
 

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

@@ -176,7 +176,7 @@ module Inferno
         if File.exist?(output_file_path)
           if old_csv == new_csv
             puts "'#{output_file_name}' file is up to date."
-            return unless unmatched_requirement_ids.present?
+            return
           else
             puts <<~MESSAGE
               #{output_file_name} file is out of date.

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

@@ -70,21 +70,24 @@ module Inferno
       #   requirement_set_id_2: [row1, row2, row 3, ...]
       # }
       def input_requirement_sets
-        requirement_set_hash = Hash.new { |hash, key| hash[key] = [] }
-        available_input_worksheets.each_with_object(requirement_set_hash) do |worksheet_file, requirement_sets|
-          worksheet = Roo::Spreadsheet.open(worksheet_file)
-          set_identifier = requirement_set_id(worksheet)
-
-          CSV.parse(
-            worksheet.sheet('Requirements').to_csv,
-            headers: true
-          ).each do |row|
-            row_hash = row.to_h.slice(*INPUT_HEADERS)
-            row_hash['Sub-Requirement(s)']&.delete_prefix!('mailto:')
-
-            requirement_sets[set_identifier] << row_hash
+        @input_requirement_sets ||=
+          begin
+            requirement_set_hash = Hash.new { |hash, key| hash[key] = [] }
+            available_input_worksheets.each_with_object(requirement_set_hash) do |worksheet_file, requirement_sets|
+              worksheet = Roo::Spreadsheet.open(worksheet_file)
+              set_identifier = requirement_set_id(worksheet)
+
+              CSV.parse(
+                worksheet.sheet('Requirements').to_csv,
+                headers: true
+              ).each do |row|
+                row_hash = row.to_h.slice(*INPUT_HEADERS)
+                row_hash['Sub-Requirement(s)']&.delete_prefix!('mailto:')
+
+                requirement_sets[set_identifier] << row_hash
+              end
+            end
           end
-        end
       end
 
       def new_requirements_csv # rubocop:disable Metrics/CyclomaticComplexity
@@ -125,6 +128,52 @@ module Inferno
         @old_requirements_csv ||= File.read(requirements_output_file_path)
       end
 
+      def missing_subrequirements
+        @missing_subrequirements =
+          {}.tap do |missing_requirements|
+            repo = Inferno::Repositories::Requirements.new
+
+            input_requirement_sets
+              .each do |requirement_set, requirements|
+                requirements.each do |requirement_hash|
+                  missing_subrequirements =
+                    Inferno::Entities::Requirement.expand_requirement_ids(requirement_hash['Sub-Requirement(s)'])
+                      .reject { |requirement_id| repo.exists? requirement_id }
+
+                  missing_subrequirements += missing_actor_subrequirements(requirement_hash['Sub-Requirement(s)'])
+
+                  next if missing_subrequirements.blank?
+
+                  id = "#{requirement_set}@#{requirement_hash['ID*']}"
+
+                  missing_requirements[id] = missing_subrequirements
+                end
+              end
+          end
+      end
+
+      def missing_actor_subrequirements(subrequirement_string)
+        return [] if subrequirement_string.blank?
+
+        return [] unless subrequirement_string.include? '#'
+
+        subrequirement_string
+          .split(',')
+          .map(&:strip)
+          .select { |requirement_string| requirement_string.include? '#' }
+          .select do |requirement_string|
+            Inferno::Entities::Requirement.expand_requirement_ids(requirement_string).blank?
+          end
+      end
+
+      def check_subrequirements
+        return if missing_subrequirements.blank?
+
+        missing_subrequirements.each do |id, subrequirement_ids|
+          puts "#{id} is missing the following sub-requirements:\n  #{subrequirement_ids.join(', ')}"
+        end
+      end
+
       def run
         check_presence_of_input_files
 
@@ -147,6 +196,10 @@ module Inferno
           File.write(requirements_output_file_path, new_requirements_csv, encoding: Encoding::UTF_8)
         end
 
+        Inferno::Application.start(:requirements)
+
+        check_subrequirements
+
         puts 'Done.'
       end
 
@@ -167,14 +220,20 @@ module Inferno
             false
           end
 
-        return if requirements_ok
+        unless requirements_ok
+          puts <<~MESSAGE
+            Check Failed. To resolve, run:
+
+                  bundle exec inferno requirements export_csv
+
+          MESSAGE
+          exit(1)
+        end
 
-        puts <<~MESSAGE
-          Check Failed. To resolve, run:
+        check_subrequirements
 
-                bundle exec inferno requirements export_csv
+        return if missing_subrequirements.blank?
 
-        MESSAGE
         exit(1)
       end
 

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

@@ -9,7 +9,7 @@ module Inferno
         field :requirement
         field :conformance
         field :actors
-        field :sub_requirements
+        field :subrequirements
         field :conditionality
         field :url, if: :field_present?
         field :not_tested_reason, if: :field_present?

data/lib/inferno/dsl/assertions.rb

@@ -66,8 +66,9 @@ module Inferno
       # Validate a FHIR resource
       #
       # @param resource [FHIR::Model]
-      # @param profile_url [String] url of the profile to validate against,
-      #   defaults to validating against the base FHIR resource
+      # @param profile_url [String] canonical url of the profile to validate against,
+      #   may include a version separated by a vertical bar (|),
+      #   and defaults to validating against the base FHIR resource type
       # @param validator [Symbol] the name of the validator to use
       # @return [void]
       def assert_valid_resource(resource: self.resource, profile_url: nil, validator: :default)

data/lib/inferno/dsl/fhir_resource_navigation.rb

@@ -147,7 +147,7 @@ module Inferno
       end
 
       def matching_pattern_identifier_slice?(slice, discriminator)
-        slice.identifier.system == discriminator[:system]
+        slice.system == discriminator[:system]
       end
 
       def matching_value_slice?(slice, discriminator)

data/lib/inferno/dsl/fhir_resource_validation.rb

@@ -1,4 +1,5 @@
 require_relative '../ext/fhir_models'
+require_relative '../feature'
 module Inferno
   module DSL
     # This module contains the methods needed to configure a validator to
@@ -19,7 +20,7 @@ module Inferno
     #         { type: 'info', message: 'everything is ok' }
     #       end
     #     end
-    #     cli_context do
+    #     validation_context do
     #       noExtensibleBindingMessages true
     #       allowExampleUrls true
     #       txServer nil
@@ -74,12 +75,12 @@ module Inferno
         #   igs("hl7.fhir.us.core#3.1.1", "hl7.fhir.us.core#6.0.0")
         # @param validator_igs [Array<String>]
         def igs(*validator_igs)
-          cli_context(igs: validator_igs) if validator_igs.any?
+          validation_context(igs: validator_igs) if validator_igs.any?
 
-          cli_context.igs
+          validation_context.igs
         end
 
-        # Set the cliContext used as part of each validation request.
+        # Set the validationContext used as part of each validation request.
         # Fields may be passed as either a Hash or block.
         # Note that all fields included here will be sent directly in requests,
         # there is no check that the fields are correct.
@@ -88,7 +89,7 @@ module Inferno
         #   # Passing fields in a block
         #   fhir_resource_validator do
         #     url 'http://example.com/validator'
-        #     cli_context do
+        #     validation_context do
         #       noExtensibleBindingMessages true
         #       allowExampleUrls true
         #       txServer nil
@@ -99,7 +100,7 @@ module Inferno
         #   # Passing fields in a Hash
         #   fhir_resource_validator do
         #     url 'http://example.org/validator'
-        #     cli_context({
+        #     validation_context({
         #       noExtensibleBindingMessages: true,
         #       allowExampleUrls: true,
         #       txServer: nil
@@ -107,19 +108,21 @@ module Inferno
         #   end
         #
         # @param definition [Hash] raw fields to set, optional
-        def cli_context(definition = nil, &)
-          if @cli_context
+        def validation_context(definition = nil, &)
+          if @validation_context
             if definition
-              @cli_context.definition.merge!(definition.deep_symbolize_keys)
+              @validation_context.definition.merge!(definition.deep_symbolize_keys)
             elsif block_given?
-              @cli_context.instance_eval(&)
+              @validation_context.instance_eval(&)
             end
           else
-            @cli_context = CliContext.new(definition || {}, &)
+            @validation_context = ValidationContext.new(definition || {}, &)
           end
-          @cli_context
+          @validation_context
         end
 
+        alias cli_context validation_context
+
         # @private
         def additional_validations
           @additional_validations ||= []
@@ -268,9 +271,13 @@ module Inferno
 
           @session_id = validator_session_id if validator_session_id
 
+          # HL7 Validator Core 6.5.19+ renamed `cliContext` to `validationContext`.
+          # This allows backward compatibility until the validator-wrapper is updated.
+          context_key = Feature.use_validation_context_key? ? :validationContext : :cliContext
+
           wrapped_resource = {
-            cliContext: {
-              **cli_context.definition,
+            context_key => {
+              **validation_context.definition,
               profiles: [profile_url]
             },
             filesToValidate: [
@@ -365,10 +372,10 @@ module Inferno
       end
 
       # @private
-      class CliContext
+      class ValidationContext
         attr_reader :definition
 
-        CLICONTEXT_DEFAULTS = {
+        VALIDATIONCONTEXT_DEFAULTS = {
           sv: '4.0.1',
           doNative: false,
           extensions: ['any'],
@@ -377,13 +384,13 @@ module Inferno
 
         # @private
         def initialize(definition, &)
-          @definition = CLICONTEXT_DEFAULTS.merge(definition.deep_symbolize_keys)
+          @definition = VALIDATIONCONTEXT_DEFAULTS.merge(definition.deep_symbolize_keys)
           instance_eval(&) if block_given?
         end
 
         # @private
         def method_missing(method_name, *args)
-          # Interpret any other method as setting a field on cliContext.
+          # Interpret any other method as setting a field on validationContext.
           # Follow the same format as `Validator.url` here:
           # only set the value if one is provided.
           # args will be an empty array if no value is provided.

data/lib/inferno/entities/requirement.rb

@@ -12,7 +12,8 @@ module Inferno
         :requirement,
         :conformance,
         :actors,
-        :sub_requirements,
+        :subrequirements,
+        :subrequirements_string,
         :conditionality,
         :not_tested_reason,
         :not_tested_details
@@ -28,6 +29,10 @@ module Inferno
         self.requirement_set = id.split(/[@#]/).first
       end
 
+      def subrequirements
+        @subrequirements ||= self.class.expand_requirement_ids(subrequirements_string, requirement_set)
+      end
+
       # Expand a comma-delimited list of requirement id references into an Array
       # of full requirement ids
       #
@@ -62,7 +67,7 @@ module Inferno
             requirement_ids =
               if actor.present?
                 return Repositories::Requirements.new.requirements_for_actor(current_set, actor).map(&:id)
-              elsif requirement_string.include? '-'
+              elsif requirement_string.include?('-') && !requirement_string.match?(/[^\d\-]/)
                 start_id, end_id = requirement_string.split('-')
                 if start_id.match?(/^\d+$/) && end_id.match?(/^\d+$/)
                   (start_id..end_id).to_a

data/lib/inferno/feature.rb

@@ -4,6 +4,10 @@ module Inferno
       def requirements_enabled?
         ENV.fetch('ENABLE_REQUIREMENTS', 'false')&.casecmp?('true')
       end
+
+      def use_validation_context_key?
+        ENV.fetch('USE_VALIDATION_CONTEXT', 'false')&.casecmp?('true')
+      end
     end
   end
 end