support validation against code system fragments

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java

@@ -112,10 +112,17 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
       if (system == null && !code.hasDisplay()) { // dealing with just a plain code (enum)
         system = systemForCodeInValueSet(code.getCode());
       }
-      if (!code.hasSystem())
+      if (!code.hasSystem()) {
+        if (options.isGuessSystem() && system == null && Utilities.isAbsoluteUrl(code.getCode())) {
+          system = "urn:ietf:rfc:3986"; // this arises when using URIs bound to value sets
+        }
         code.setSystem(system);
+      }
       inExpansion = checkExpansion(code);
       CodeSystem cs = context.fetchCodeSystem(system);
+      if (cs == null) {
+        cs = findSpecialCodeSystem(system);
+      }
       if (cs == null) {
         warningMessage = "Unable to resolve system "+system+" - system is not specified or implicit";
         if (!inExpansion)
@@ -123,7 +130,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
       }
       if (cs!=null && cs.getContent() != CodeSystemContentMode.COMPLETE) {
         warningMessage = "Unable to resolve system "+system+" - system is not complete";
-        if (!inExpansion)
+        if (!inExpansion && cs.getContent() != CodeSystemContentMode.FRAGMENT) // we're going to give it a go if it's a fragment
           throw new FHIRException(warningMessage);
       }
 
@@ -147,6 +154,17 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
     return res;
   }
 
+  private CodeSystem findSpecialCodeSystem(String system) {
+    if ("urn:ietf:rfc:3986".equals(system)) {
+      CodeSystem cs = new CodeSystem();
+      cs.setUrl(system);
+      cs.setUserData("tx.cs.special", new URICodeSystem());
+      cs.setContent(CodeSystemContentMode.COMPLETE);
+      return cs; 
+    }
+    return null;
+  }
+
   boolean checkExpansion(Coding code) {
     if (valueset==null || !valueset.hasExpansion())
       return false;
@@ -164,9 +182,14 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
   }
 
   private ValidationResult validateCode(Coding code, CodeSystem cs) {
-    ConceptDefinitionComponent cc = findCodeInConcept(cs.getConcept(), code.getCode());
+    ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode());
-    if (cc == null)
+    if (cc == null) {
-      return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_, gen(code), cs.getUrl()));
+      if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
+        return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, gen(code), cs.getUrl()));        
+      } else {
+        return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_, gen(code), cs.getUrl()));
+      }
+    }
     if (code.getDisplay() == null)
       return new ValidationResult(cc);
     CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java

@@ -419,6 +419,7 @@ public class I18nConstants {
   public final static String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__ = "Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__";
   public final static String DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF_ = "Display_Name_for__should_be_one_of__instead_of_";
   public final static String UNKNOWN_CODE__IN_ = "Unknown_Code__in_";
+  public final static String UNKNOWN_CODE__IN_FRAGMENT = "UNKNOWN_CODE__IN_FRAGMENT";
   public final static String CODE_FOUND_IN_EXPANSION_HOWEVER_ = "Code_found_in_expansion_however_";
   public final static String NONE_OF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_ = "None_of_the_provided_codes_are_in_the_value_set_";
   public final static String CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE = "Coding_has_no_system__cannot_validate";

org.hl7.fhir.utilities/src/main/resources/Messages.properties

@@ -419,6 +419,7 @@ Error_parsing_ = Error parsing {0}:{1}
 Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__ = Unable to connect to terminology server. Use parameter ''-tx n/a'' tun run without using terminology services to validate LOINC, SNOMED, ICD-X etc. Error = {0}
 Display_Name_for__should_be_one_of__instead_of_ = Display Name for {0}#{1} should be one of ''{2}'' instead of ''{3}''
 Unknown_Code__in_ = Unknown Code {0} in {1}
+UNKNOWN_CODE__IN_FRAGMENT = Unknown Code {0} in {1} - note that the code system is labelled as a fragment, so the code may be valid in some other fragment
 Code_found_in_expansion_however_ = Code found in expansion, however: {0}
 None_of_the_provided_codes_are_in_the_value_set_ = None of the provided codes are in the value set {0}
 Coding_has_no_system__cannot_validate = Coding has no system - cannot validate