inferno_core 0.6.13 → 0.6.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3b6ca0be7f115ec7578f07efdb81f51301ffc58011257839439325a0f232f3dd
-  data.tar.gz: 79c99071c6d89aafea8234c9fea372efbbaf4835f39da46bad226a8b12a317b3
+  metadata.gz: be97c34b62bf28dc41266ecc22d01ccb2b8548a75150507ea72fff5aa76f6b17
+  data.tar.gz: 2f4121330b353d2f425e1be20f3895a1f256b8f20a825cc5c26adc9aa85f0898
 SHA512:
-  metadata.gz: bb251b81e0232761cdddd83603a00d7d16844c61a8c80315b4a239a2f3ff1a6305700bd9c7f352d8c179773ecc45e5d5f824d08f3c00438f4cf460069cb0ae16
-  data.tar.gz: f01952a5cd0cd31c5e6f35901409581cd047d7b6bd099865efa9bebfe40450d115c299266b1c700a7fd7cceb7b20b15a0e8635e6ff482e27193af81030d7b400
+  metadata.gz: eded37149214782930c42e8e672e768eaf0e07411fba2ad9e8f96fad282ff0ff31aee18cab668592ea355a6ddafdfd1c4128d1c04de639e24aa3968a79026ac7
+  data.tar.gz: 4322a86fc7f289cfc3cc92e70d0926c7dd79a3ce6941f8479c6096ffdcd3718a7f59e17479031d50e2a0a24cbc0e6bd632e8c31ec9cf00fdad317351176524f4

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

@@ -12,6 +12,11 @@ module Inferno
       LONGDESC
       def export_csv
         ENV['NO_DB'] = 'true'
+
+        require_relative '../../../inferno'
+
+        Inferno::Application.start(:requirements)
+
         RequirementsExporter.new.run
       end
 
@@ -22,6 +27,11 @@ module Inferno
       LONGDESC
       def check
         ENV['NO_DB'] = 'true'
+
+        require_relative '../../../inferno'
+
+        Inferno::Application.start(:requirements)
+
         RequirementsExporter.new.run_check
       end
 
@@ -66,7 +76,7 @@ module Inferno
           RequirementsCoverageChecker.new(test_suite_id).run_check
         else
           Inferno::Repositories::TestSuites.all.each do |test_suite|
-            if Object.const_source_location(test_suite.to_s).first.start_with?(Dir.pwd, 'lib')
+            if Object.const_source_location(test_suite.to_s).first.start_with?(File.join(Dir.pwd, 'lib'))
               RequirementsCoverageChecker.new(test_suite.id).run_check
             end
           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               #{output_file_name} file is out of date.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_sub_requirements
+        @missing_sub_requirements =
+          {}.tap do |missing_requirements|
+            repo = Inferno::Repositories::Requirements.new
+
+            input_requirement_sets
+              .each do |requirement_set, requirements|
+                requirements.each do |requirement_hash|
+                  missing_sub_requirements =
+                    Inferno::Entities::Requirement.expand_requirement_ids(requirement_hash['Sub-Requirement(s)'])
+                      .reject { |requirement_id| repo.exists? requirement_id }
+
+                  missing_sub_requirements += missing_actor_sub_requirements(requirement_hash['Sub-Requirement(s)'])
+
+                  next if missing_sub_requirements.blank?
+
+                  id = "#{requirement_set}@#{requirement_hash['ID*']}"
+
+                  missing_requirements[id] = missing_sub_requirements
+                end
+              end
+          end
+      end
+
+      def missing_actor_sub_requirements(sub_requirement_string)
+        return [] if sub_requirement_string.blank?
+
+        return [] unless sub_requirement_string.include? '#'
+
+        sub_requirement_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_sub_requirements
+        return if missing_sub_requirements.blank?
+
+        missing_sub_requirements.each do |id, sub_requirement_ids|
+          puts "#{id} is missing the following sub-requirements:\n  #{sub_requirement_ids.join(', ')}"
+        end
+      end
+
       def run
         check_presence_of_input_files
 
@@ -147,6 +196,8 @@ module Inferno
           File.write(requirements_output_file_path, new_requirements_csv, encoding: Encoding::UTF_8)
         end
 
+        check_sub_requirements
+
         puts 'Done.'
       end
 
@@ -167,14 +218,20 @@ 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_sub_requirements
 
-                bundle exec inferno requirements export_csv
+        return if missing_sub_requirements.blank?
 
-        MESSAGE
         exit(1)
       end
 

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)