Various corrections to address attributes being non-compliant with STU3

fixtures/stu3/terminology/codesystem-simple.xml

@@ -53,12 +53,6 @@
       This is not an absolute requirement, but it may be enforced by some 
       servers - for instance, the HL7 valueset registry will.     -->
   <url value="http://hl7.org/fhir/CodeSystem/example-crucible"/>
-<!--    an imaginary identifier. This is a non FHIR identifier - might be used in a 
-	  v2 context (though you always need to translate namespaces for v2)    -->
-  <identifier>
-    <system value="http://acme.com/identifiers/codesystems"/>
-    <value value="internal-cholesterol-inl"/>
-  </identifier>
 <!--    for version, we are going to simply use the day of publication. This is also 
     arbitrary - whatever is here is what people use to refer to the version. 
     Could also be a UUID too. Note that you should change the identify of the code 

lib/resource_generator.rb

@@ -772,10 +772,7 @@ def self.apply_invariants!(resource)
           #   i.maxLength = nil if !['boolean', 'decimal', 'integer', 'string', 'text', 'url'].include?(i.type)
           # end
         when FHIR::QuestionnaireResponse
-          resource.item.each do |i|
-            i.item = nil
-            i.answer.each {|q|q.valueBoolean = true if !q.value }
-          end
+          fix_questionnaire_response_items(resource.item)
         when FHIR::Range
           # validate that the low/high values in the range are correct (e.g. the low value is not higher than the high value)
           if resource.low && resource.high
@@ -1559,10 +1556,7 @@ def self.apply_invariants!(resource)
             i.maxLength = nil if !['boolean', 'decimal', 'integer', 'string', 'text', 'url'].include?(i.type)
           end
         when FHIR::STU3::QuestionnaireResponse
-          resource.item.each do |i|
-            i.item = nil
-            i.answer.each {|q|q.valueBoolean = true if !q.value }
-          end
+          fix_questionnaire_response_items(resource.item)
         when FHIR::STU3::Range
           # validate that the low/high values in the range are correct (e.g. the low value is not higher than the high value)
           if resource.low && resource.high
@@ -2267,6 +2261,36 @@ def self.apply_invariants!(resource)
         end
       end
 
+      # Recursively fixes a QuestionnaireResponse item tree so it can be accepted
+      # by a strict FHIR parser.
+      #
+      # The generated tree can be arbitrarily deep via two nesting axes:
+      #   item.answer[].item[]   — items nested inside an answer
+      #   item.item[]            — direct sub-item groups on an item
+      #
+      # Two problems are corrected at every level:
+      #   1. Answers with no value are given `valueBoolean = true`.  A strict parser
+      #      rejects answer objects that are completely empty (`{}`).
+      #   2. Direct sub-item groups (`item.item`) are removed.  They are often
+      #      generated empty or with invalid content that would fail validation.
+      #
+      # Ordering matters: `answer.item` is recursed BEFORE `item.item` is cleared,
+      # because answer-nested items may themselves contain answers that need fixing.
+      # Clearing `item.item` first would not affect `answer.item`, but fixing
+      # `answer.item` last would process items that are immediately discarded —
+      # so the current order keeps the logic clear: fix answers deeply first, then drop
+      # the direct sub-groups.
+      def self.fix_questionnaire_response_items(items)
+        return if items.nil? || items.empty?
+        items.each do |item|
+          item.answer.each do |answer|
+            answer.valueBoolean = true unless answer.value
+            fix_questionnaire_response_items(answer.item) unless answer.item.nil?
+          end
+          item.item = nil
+        end
+      end
+
     end
   end
 end

lib/tests/suites/connectathon_attachment_track_test.rb

@@ -59,7 +59,7 @@ def teardown
             requires resource: 'Communication', methods: ['create']
           }
           comm = FHIR::STU3::Communication.new()
-          comm.subject = [@records[:patient].to_reference]
+          comm.subject = @records[:patient].to_reference
           comm.recipient = [@records[:practitioner].to_reference]
           comm.status = 'preparation'
 
@@ -69,9 +69,9 @@ def teardown
           comm_att.title = @attachments[att_type]
 
           payload = FHIR::STU3::Communication::Payload.new
-          payload.contentAttachment = [comm_att]
+          payload.contentAttachment = comm_att
 
-          comm.payload = payload
+          comm.payload = [payload]
           create_object(comm, "comm_#{att_type}")
         end
 
@@ -103,8 +103,8 @@ def teardown
           assert comm_req, 'No CommunicationRequest returned from server'
 
           comm = FHIR::STU3::Communication.new()
-          comm.subject = [comm_req.subject]
-          comm.recipient = [comm_req.sender]
+          comm.subject = comm_req.subject
+          comm.recipient = [comm_req.sender].compact
           comm.basedOn = [comm_req.to_reference]
           comm.status = 'preparation'
 
@@ -114,9 +114,9 @@ def teardown
           comm_att.title = @attachments[att_type]
 
           payload = FHIR::STU3::Communication::Payload.new
-          payload.contentAttachment = [comm_att]
+          payload.contentAttachment = comm_att
 
-          comm.payload = payload
+          comm.payload = [payload]
           create_object(comm, "comm_#{att_type}")
         end
       end

lib/tests/suites/connectathon_genomics_track_test.rb

@@ -63,7 +63,7 @@ def teardown
 
         observation.subject = @records[:patient].to_reference
         observation.specimen = @records[:specimen_register_create].to_reference
-        observation.performer = @records[:practitioner].to_reference
+        observation.performer = [@records[:practitioner].to_reference]
         create_object(observation, :observation_register_create)
       end
 
@@ -127,11 +127,11 @@ def teardown
         create_object(specimen, :family_specimen)
 
         diag_report = @resources.diagnostic_familyhistory
-        diag_report.result = @records[:family_observation].to_reference
+        diag_report.result = [@records[:family_observation].to_reference]
         diag_report.subject = @records[:family_patient].to_reference
         diag_report.performer = [ FHIR::STU3::DiagnosticReport::Performer.new ]
         diag_report.performer.first.actor = @records[:practitioner].to_reference
-        diag_report.specimen = @records[:family_specimen].to_reference
+        diag_report.specimen = [@records[:family_specimen].to_reference]
         create_object(diag_report, :family_report)
 
         reply = @client.read FHIR::STU3::FamilyMemberHistory, @records[:family_member_history].id
@@ -162,7 +162,7 @@ def teardown
 
 
         dw_obs = @resources.observation_datawarehouse
-        dw_obs.performer = @records[:practitioner].to_reference
+        dw_obs.performer = [@records[:practitioner].to_reference]
         dw_obs.subject = @records[:family_patient].to_reference
         dw_obs.specimen = @records[:family_specimen].to_reference
         create_object(dw_obs, :dw_obs)

lib/tests/suites/connectathon_lab_order_track.rb

@@ -178,7 +178,7 @@ def create_diagnostic_report(specimen_name, observation_fixture_paths, diagnosti
           observation = @resources.load_fixture(obs, :xml)
           observation.specimen = @records[specimen_name].to_reference
           observation.subject = @records[:patient].to_reference
-          observation.performer = @records[:performer].to_reference
+          observation.performer = [@records[:performer].to_reference]
           observation_name = "#{dr_name}_observation_#{index}".to_sym
           create_object(observation, observation_name)
           diag_report.result << @records[observation_name].to_reference