Fix up support for inactive codes and fix error message syntax

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

@@ -544,9 +544,10 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
       if (s.startsWith("version=")) {
         if (version == null)
         version = s.substring(8);
-        else if (!version.equals(s.substring(8))) 
+        else if (!version.equals(s.substring(8))) {
           throw new DefinitionException(formatMessage(I18nConstants.VERSION_MISMATCH_THE_CONTEXT_HAS_VERSION__LOADED_AND_THE_NEW_CONTENT_BEING_LOADED_IS_VERSION_, version, s.substring(8)));
         }
+      }
       if (s.startsWith("revision="))
         revision = s.substring(9);
       if (s.startsWith("date="))

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

@@ -498,6 +498,14 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
     }    
   }
 
+  public void copyNewExtensions(org.hl7.fhir.r5.model.Element src, String... urls) {
+    for (Extension e : src.getExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls) && !!hasExtension(e.getUrl())) {
+        addExtension(e.copy());
+      }
+    }    
+  }
+  
   
 // end addition
 

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

@@ -369,6 +369,10 @@ public class CodeSystemUtilities {
       if ("inactive".equals(p.getCode()) && p.hasValueBooleanType()) {
         return p.getValueBooleanType().getValue();
       }
+      if ("inactive".equals(p.getCode()) && p.hasValueCodeType()) {
+        String code = p.getValueCodeType().primitiveValue();
+        return "true".equals(code);
+      }
     }
     return false;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/validation/ValidationProcessInfo.java

@@ -29,7 +29,7 @@ public class ValidationProcessInfo {
     return issues;
   }
   public void addIssue(List<OperationOutcomeIssueComponent> issues) {
-    issues.addAll(issues);
+    this.issues.addAll(issues);
     
   }
   public boolean hasErrors() {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/validation/ValueSetValidator.java

@@ -214,7 +214,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
           }
         } else {
           c.setUserData("cs", cs);
-          res = validateCode(path+".coding["+i+"]", c, cs, vcc);
+          res = validateCode(path+".coding["+i+"]", c, cs, vcc, info);
         }
         info.getIssues().addAll(res.getIssues());
         i++;
@@ -349,6 +349,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
     boolean inExpansion = false;
     boolean inInclude = false;
     List<OperationOutcomeIssueComponent> issues = new ArrayList<>();
+    ValidationProcessInfo info = new ValidationProcessInfo(issues);
     VersionInfo vi = new VersionInfo(this);
     checkCanonical(issues, path, valueset);
 
@@ -439,7 +440,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
           // we can't validate that here. 
           throw new FHIRException("Unable to evaluate based on empty code system");
         }
-        res = validateCode(path, code, cs, null);
+        res = validateCode(path, code, cs, null, info);
         res.setIssues(issues);
       } else if (cs == null && valueset.hasExpansion() && inExpansion) {
         // we just take the value set as face value then
@@ -460,7 +461,6 @@ public class ValueSetValidator extends ValueSetProcessBase {
     }
     String wv = vi.getVersion(system, code.getVersion());
 
-    ValidationProcessInfo info = new ValidationProcessInfo(issues);
     
     // then, if we have a value set, we check it's in the value set
     if (valueset != null && options.getValueSetMode() != ValueSetMode.NO_MEMBERSHIP_CHECK) {
@@ -633,7 +633,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
     return false;
   }
 
-  private ValidationResult validateCode(String path, Coding code, CodeSystem cs, CodeableConcept vcc) {
+  private ValidationResult validateCode(String path, Coding code, CodeSystem cs, CodeableConcept vcc, ValidationProcessInfo info) {
     ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode(), allAltCodes);
     if (cc == null) {
       if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
@@ -648,6 +648,9 @@ public class ValueSetValidator extends ValueSetProcessBase {
     if (vcc != null) {
       vcc.addCoding(vc);
     }
+    if (CodeSystemUtilities.isInactive(cs, cc)) {
+      info.addIssue(makeIssue(IssueSeverity.WARNING, IssueType.EXPIRED, path, context.formatMessage(I18nConstants.INACTIVE_CODE_WARNING, cc.getCode())));
+    }
     boolean ws = false;    
     if (code.getDisplay() == null) {
       return new ValidationResult(code.getSystem(), cs.getVersion(), cc, vc.getDisplay());
@@ -1081,6 +1084,12 @@ public class ValueSetValidator extends ValueSetProcessBase {
       }
     } else {
       checkCanonical(info.getIssues(), path, cs);
+      if (valueset.getCompose().hasInactive() && !valueset.getCompose().getInactive()) {
+        if (CodeSystemUtilities.isInactive(cs, code)) {
+          return false;
+        }
+      }
+      
       if (vsi.hasFilter()) {
         ok = true;
         for (ConceptSetFilterComponent f : vsi.getFilter()) {

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

@@ -286,34 +286,4 @@ public class XVerExtensionManager {
     }
   }
 
-  public String getReference(String url) {
-    String version = getVersion(url);
-    String base = VersionUtilities.getSpecUrl(version);
-    if (base == null) {
-      return null;
-    } else {
-      String path = url.substring(url.indexOf("-")+1);
-      if (!path.contains(".")) {
-        return null;
-      }
-      String type = path.substring(0, path.indexOf("."));
-      if (Utilities.existsInList(type, "Annotation", "Attachment", "Identifier", "CodeableConcept", "Coding", "Quantity", "Duration", "Range", "Period", "Ratio", "RatioRange", "SampledData", "Signature", "HumanName", "Address", "ContactPoint", "Timing")) {
-        return Utilities.pathURL(base, "datatypes-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
-      }
-      if (Utilities.existsInList(type, "Element", "BackboneElement", "BackboneType", "PrimitiveType", "DataType", "Base")) {
-        return Utilities.pathURL(base, "types-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
-      }
-      if (Utilities.existsInList(type, "UsageContext", "RelatedArtifact", "DataRequirement", "ParameterDefinition", "TriggerDefinition", "Expression", "ContactDetail", "ExtendedContactDetail", "VirtualServiceDetail", "Availability", "MonetaryComponent", "Contributor")) {
-        return Utilities.pathURL(base, "metadatatypes-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
-      }
-      if (Utilities.existsInList(type, "Reference", "CodeableReference")) {
-        return Utilities.pathURL(base, "references-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
-      }
-      if (Utilities.existsInList(type, "Meta")) {
-        return Utilities.pathURL(base, "resource-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
-      }
-      return Utilities.pathURL(base, type.toLowerCase()+"-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
-    }
-  }
-
 }

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

@@ -954,9 +954,7 @@ public class I18nConstants {
   public static final String MSG_DEPRECATED = "MSG_DEPRECATED";
   public static final String MSG_WITHDRAWN = "MSG_WITHDRAWN";
   public static final String MSG_RETIRED = "MSG_RETIRED";
-
+  public static final String INACTIVE_CODE_WARNING = "INACTIVE_CODE_WARNING";
-
-
 }
 
 

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

@@ -171,7 +171,7 @@ Terminology_TX_NoValid_13 = The Coding provided ({2}) is not in the value set {0
 Terminology_TX_NoValid_14 = The Coding provided ({2}) is not in the value set {0}, and a code is recommended to come from this value set. {1}
 Terminology_TX_NoValid_15 = The value provided (''{0}'') could not be validated in the absence of a terminology server
 Terminology_TX_NoValid_15A = The value provided (''{0}'') could not be validated because the code system {1} is not known
-Terminology_TX_NoValid_16 = The value provided (''{0}'') is not in the value set {1}, and a code is required from this value set){2}
+Terminology_TX_NoValid_16 = The value provided (''{0}'') is not in the value set {1}, and a code is required from this value set {2}
 Terminology_TX_NoValid_17 = The value provided (''{0}'') is not in the value set {1}, and a code should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) {2}
 Terminology_TX_NoValid_18 = The value provided (''{0}'') is not in the value set {1}, and a code is recommended to come from this value set){2}
 Terminology_TX_NoValid_2_CC = None of the codings provided are in the value set {0}, and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = {1})
@@ -1011,3 +1011,4 @@ SD_EXTENSION_URL_MISMATCH = The fixed value for the extension URL is {1} which d
 MSG_DEPRECATED = Reference to deprecated item {0}
 MSG_WITHDRAWN = Reference to withdrawn item {0}
 MSG_RETIRED = Reference to retired item {0}
+INACTIVE_CODE_WARNING = The code ''{0}'' is valid but is not active