rendering improvemnets for code system

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java

@@ -800,8 +800,12 @@ public abstract class BaseWorkerContext implements IWorkerContext {
   public Resource fetchResourceById(String type, String uri) {
     synchronized (lock) {
       String[] parts = uri.split("\\/");
-      if (!Utilities.noString(type) && parts.length == 1)
+      if (!Utilities.noString(type) && parts.length == 1) {
-        return allResourcesById.get(type).get(parts[0]);
+        if (allResourcesById.containsKey(type))
+          return allResourcesById.get(type).get(parts[0]);
+        else
+          return null;
+      }
       if (parts.length >= 2) {
         if (!Utilities.noString(type))
           if (!type.equals(parts[parts.length-2])) 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Constants.java

@@ -59,4 +59,5 @@ public class Constants {
   public final static String BUILD_ID = "e0e3caf9ba";
   public final static String DATE = "Thu Dec 13 14:07:26 AEDT 2018";
   public final static String URI_REGEX = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?";
+  public final static String LOCAL_REF_REGEX = "(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}";
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java

@@ -3369,7 +3369,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
     return "??Lang";
   }
  
-  private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean version, boolean deprecated, List<UsedConceptMap> maps, String system, CodeSystem cs, String lang) {
+  private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean version, boolean deprecated, List<UsedConceptMap> maps, String system, CodeSystem cs, String lang) throws FHIRFormatError, DefinitionException, IOException {
     boolean hasExtensions = false;
     XhtmlNode tr = t.tr();
     XhtmlNode td = tr.td();
@@ -3417,7 +3417,10 @@ public class NarrativeGenerator implements INarrativeGenerator {
     if (c != null && 
         c.hasDefinitionElement()) {
       if (lang == null) {
-        td.addText(c.getDefinition());
+        if (hasMarkdownInDefinitions(cs))
+          addMarkdown(td, c.getDefinition());
+        else
+          td.addText(c.getDefinition());
       } else if (lang.equals("*")) {
         boolean sl = false;
         for (ConceptDefinitionDesignationComponent cd : c.getDesignation()) 
@@ -3534,6 +3537,10 @@ public class NarrativeGenerator implements INarrativeGenerator {
   }
 
 
+  private boolean hasMarkdownInDefinitions(CodeSystem cs) {
+    return ToolingExtensions.readBoolExtension(cs, "http://hl7.org/fhir/StructureDefinition/codesystem-use-markdown");
+  }
+
   private String makeAnchor(String codeSystem, String code) {
     String s = codeSystem+'-'+code;
     StringBuilder b = new StringBuilder();