Merge pull request #1454 from hapifhir/2023-10-gg-cda-fixes-2

2023 10 gg cda fixes 2

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertorConstants.java

@@ -41,7 +41,7 @@ public class VersionConvertorConstants {
   public final static String MODIFIER_REASON_LEGACY = "No Modifier Reason provideed in previous versions of FHIR";
   public final static String PROFILE_EXTENSION = "http://hl7.org/fhir/4.0/StructureDefinition/extension-ElementDefinition.type.profile";
   public final static String IG_CONFORMANCE_MESSAGE_EVENT = "http://hl7.org/fhir/1.0/StructureDefinition/extension-Conformance.messaging.event";
-  public static final String EXT_OLD_CONCEPTMAP_EQUIVALENCE = "http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.element.target.equivalence";
+  public static final String EXT_OLD_CONCEPTMAP_EQUIVALENCE = "http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.group.element.target.equivalence";
   public static final String EXT_ACTUAL_RESOURCE_NAME = "http://hl7.org/fhir/tools/StructureDefinition/original-resource-name";
   public static final String EXT_QUESTIONNAIRE_ITEM_TYPE_ORIGINAL = QuestionnaireRenderer.EXT_QUESTIONNAIRE_ITEM_TYPE_ORIGINAL;
   public static final String EXT_NAMINGSYSTEM_TITLE = "http://hl7.org/fhir/5.0/StructureDefinition/extension-NamingSystem.title";

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv10_50/resources10_50/ConceptMap10_50.java

@@ -148,13 +148,13 @@ public class ConceptMap10_50 {
     return tgt;
   }
 
-  public static org.hl7.fhir.dstu2.model.Enumeration<ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src) throws FHIRException {
+  public static org.hl7.fhir.dstu2.model.Enumeration<ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent ccm) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     org.hl7.fhir.dstu2.model.Enumeration<ConceptMapEquivalence> tgt = new org.hl7.fhir.dstu2.model.Enumeration<ConceptMapEquivalence>(new org.hl7.fhir.dstu2.model.Enumerations.ConceptMapEquivalenceEnumFactory());
-    ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().copyElement(src, tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
+    ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().copyElement(src, tgt);
-    if (src.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
+    if (ccm.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
-      tgt.setValueAsString(src.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
+      tgt.setValueAsString(ccm.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
     } else {
       switch (src.getValue()) {
         case EQUIVALENT:
@@ -177,12 +177,12 @@ public class ConceptMap10_50 {
     return tgt;
   }
 
-  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.dstu2.model.Enumeration<ConceptMapEquivalence> src) throws FHIRException {
+  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.dstu2.model.Enumeration<ConceptMapEquivalence> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent tgtCtxt) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     Enumeration<ConceptMapRelationship> tgt = new Enumeration<ConceptMapRelationship>(new Enumerations.ConceptMapRelationshipEnumFactory());
     ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().copyElement(src, tgt);
-    ToolingExtensions.setCodeExtension(tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
+    ToolingExtensions.setCodeExtensionMod(tgtCtxt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
     switch (src.getValue()) {
       case EQUIVALENT:
         tgt.setValue(org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship.EQUIVALENT);
@@ -283,12 +283,12 @@ public class ConceptMap10_50 {
     if (src == null || src.isEmpty())
       return null;
     org.hl7.fhir.dstu2.model.ConceptMap.TargetElementComponent tgt = new org.hl7.fhir.dstu2.model.ConceptMap.TargetElementComponent();
-    ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().copyBackboneElement(src,tgt);
+    ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().copyBackboneElement(src,tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
     tgt.setCodeSystem(g.getTarget());
     if (src.hasCodeElement())
       tgt.setCodeElement(Code10_50.convertCode(src.getCodeElement()));
     if (src.hasRelationship())
-      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement()));
+      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement(), src));
     if (src.hasCommentElement())
       tgt.setCommentsElement(String10_50.convertString(src.getCommentElement()));
     for (org.hl7.fhir.r5.model.ConceptMap.OtherElementComponent t : src.getDependsOn())
@@ -306,7 +306,7 @@ public class ConceptMap10_50 {
     if (src.hasCodeElement())
       tgt.setCodeElement(Code10_50.convertCode(src.getCodeElement()));
     if (src.hasEquivalence())
-      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement()));
+      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement(), tgt));
     if (src.hasCommentsElement())
       tgt.setCommentElement(String10_50.convertString(src.getCommentsElement()));
     for (org.hl7.fhir.dstu2.model.ConceptMap.OtherElementComponent t : src.getDependsOn())

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv14_50/resources14_50/ConceptMap14_50.java

@@ -151,13 +151,13 @@ public class ConceptMap14_50 {
     return tgt;
   }
 
-  public static org.hl7.fhir.dstu2016may.model.Enumeration<ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src) throws FHIRException {
+  public static org.hl7.fhir.dstu2016may.model.Enumeration<ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent ccm) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     org.hl7.fhir.dstu2016may.model.Enumeration<ConceptMapEquivalence> tgt = new org.hl7.fhir.dstu2016may.model.Enumeration<ConceptMapEquivalence>(new org.hl7.fhir.dstu2016may.model.Enumerations.ConceptMapEquivalenceEnumFactory());
-    ConversionContext14_50.INSTANCE.getVersionConvertor_14_50().copyElement(src, tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
+    ConversionContext14_50.INSTANCE.getVersionConvertor_14_50().copyElement(src, tgt);
-    if (src.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
+    if (ccm.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
-      tgt.setValueAsString(src.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
+      tgt.setValueAsString(ccm.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
     } else {
       switch (src.getValue()) {
         case EQUIVALENT:
@@ -180,12 +180,12 @@ public class ConceptMap14_50 {
     return tgt;
   }
 
-  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.dstu2016may.model.Enumeration<ConceptMapEquivalence> src) throws FHIRException {
+  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.dstu2016may.model.Enumeration<ConceptMapEquivalence> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent tgtCtxt) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     Enumeration<ConceptMapRelationship> tgt = new Enumeration<ConceptMapRelationship>(new Enumerations.ConceptMapRelationshipEnumFactory());
     ConversionContext14_50.INSTANCE.getVersionConvertor_14_50().copyElement(src, tgt);
-    ToolingExtensions.setCodeExtension(tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
+    ToolingExtensions.setCodeExtensionMod(tgtCtxt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
     switch (src.getValue()) {
       case EQUIVALENT:
         tgt.setValue(org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship.EQUIVALENT);
@@ -293,13 +293,13 @@ public class ConceptMap14_50 {
     if (src == null || src.isEmpty())
       return null;
     org.hl7.fhir.dstu2016may.model.ConceptMap.TargetElementComponent tgt = new org.hl7.fhir.dstu2016may.model.ConceptMap.TargetElementComponent();
-    ConversionContext14_50.INSTANCE.getVersionConvertor_14_50().copyBackboneElement(src,tgt);
+    ConversionContext14_50.INSTANCE.getVersionConvertor_14_50().copyBackboneElement(src,tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
     if (g.hasTarget())
       tgt.setSystem(g.getTarget());
     if (src.hasCode())
       tgt.setCodeElement(Code14_50.convertCode(src.getCodeElement()));
     if (src.hasRelationship())
-      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement()));
+      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement(), src));
     if (src.hasComment())
       tgt.setCommentsElement(String14_50.convertString(src.getCommentElement()));
     for (org.hl7.fhir.r5.model.ConceptMap.OtherElementComponent t : src.getDependsOn())
@@ -317,7 +317,7 @@ public class ConceptMap14_50 {
     if (src.hasCode())
       tgt.setCodeElement(Code14_50.convertCode(src.getCodeElement()));
     if (src.hasEquivalence())
-      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement()));
+      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement(), tgt));
     if (src.hasComments())
       tgt.setCommentElement(String14_50.convertString(src.getCommentsElement()));
     for (org.hl7.fhir.dstu2016may.model.ConceptMap.OtherElementComponent t : src.getDependsOn())

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv30_50/resources30_50/ConceptMap30_50.java

@@ -247,13 +247,13 @@ public class ConceptMap30_50 {
     return tgt;
   }
 
-  public static org.hl7.fhir.dstu3.model.Enumeration<ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src) throws FHIRException {
+  public static org.hl7.fhir.dstu3.model.Enumeration<ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent ccm) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     org.hl7.fhir.dstu3.model.Enumeration<ConceptMapEquivalence> tgt = new org.hl7.fhir.dstu3.model.Enumeration<ConceptMapEquivalence>(new org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalenceEnumFactory());
-    ConversionContext30_50.INSTANCE.getVersionConvertor_30_50().copyElement(src, tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
+    ConversionContext30_50.INSTANCE.getVersionConvertor_30_50().copyElement(src, tgt);
-    if (src.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
+    if (ccm.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
-      tgt.setValueAsString(src.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
+      tgt.setValueAsString(ccm.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
     } else {
       switch (src.getValue()) {
         case EQUIVALENT:
@@ -279,12 +279,12 @@ public class ConceptMap30_50 {
     return tgt;
   }
 
-  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.dstu3.model.Enumeration<ConceptMapEquivalence> src) throws FHIRException {
+  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.dstu3.model.Enumeration<ConceptMapEquivalence> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent tgtCtxt) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     Enumeration<ConceptMapRelationship> tgt = new Enumeration<ConceptMapRelationship>(new Enumerations.ConceptMapRelationshipEnumFactory());
     ConversionContext30_50.INSTANCE.getVersionConvertor_30_50().copyElement(src, tgt);
-    ToolingExtensions.setCodeExtension(tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
+    ToolingExtensions.setCodeExtensionMod(tgtCtxt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
     switch (src.getValue()) {
       case EQUIVALENT:
         tgt.setValue(org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship.EQUIVALENT);
@@ -402,7 +402,7 @@ public class ConceptMap30_50 {
     if (src.hasDisplay())
       tgt.setDisplayElement(String30_50.convertString(src.getDisplayElement()));
     if (src.hasEquivalence())
-      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement()));
+      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement(), tgt));
     if (src.hasComment())
       tgt.setCommentElement(String30_50.convertString(src.getCommentElement()));
     for (org.hl7.fhir.dstu3.model.ConceptMap.OtherElementComponent t : src.getDependsOn())
@@ -416,13 +416,13 @@ public class ConceptMap30_50 {
     if (src == null)
       return null;
     org.hl7.fhir.dstu3.model.ConceptMap.TargetElementComponent tgt = new org.hl7.fhir.dstu3.model.ConceptMap.TargetElementComponent();
-    ConversionContext30_50.INSTANCE.getVersionConvertor_30_50().copyBackboneElement(src,tgt);
+    ConversionContext30_50.INSTANCE.getVersionConvertor_30_50().copyBackboneElement(src,tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
     if (src.hasCode())
       tgt.setCodeElement(Code30_50.convertCode(src.getCodeElement()));
     if (src.hasDisplay())
       tgt.setDisplayElement(String30_50.convertString(src.getDisplayElement()));
     if (src.hasRelationship())
-      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement()));
+      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement(), src));
     if (src.hasComment())
       tgt.setCommentElement(String30_50.convertString(src.getCommentElement()));
     for (org.hl7.fhir.r5.model.ConceptMap.OtherElementComponent t : src.getDependsOn())

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/resources40_50/ConceptMap40_50.java

@@ -242,7 +242,7 @@ public class ConceptMap40_50 {
     if (src.hasDisplay())
       tgt.setDisplayElement(String40_50.convertString(src.getDisplayElement()));
     if (src.hasEquivalence())
-      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement()));
+      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement(), tgt));
     if (src.hasComment())
       tgt.setCommentElement(String40_50.convertString(src.getCommentElement()));
     for (org.hl7.fhir.r4.model.ConceptMap.OtherElementComponent t : src.getDependsOn())
@@ -256,13 +256,13 @@ public class ConceptMap40_50 {
     if (src == null)
       return null;
     org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent tgt = new org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent();
-    ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().copyBackboneElement(src, tgt);
+    ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().copyBackboneElement(src, tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
     if (src.hasCode())
       tgt.setCodeElement(Code40_50.convertCode(src.getCodeElement()));
     if (src.hasDisplay())
       tgt.setDisplayElement(String40_50.convertString(src.getDisplayElement()));
     if (src.hasRelationship())
-      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement()));
+      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement(), src));
     else
       tgt.setEquivalence(ConceptMapEquivalence.RELATEDTO);
     if (src.hasComment())
@@ -274,13 +274,13 @@ public class ConceptMap40_50 {
     return tgt;
   }
 
-  public static org.hl7.fhir.r4.model.Enumeration<ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src) throws FHIRException {
+  public static org.hl7.fhir.r4.model.Enumeration<ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent ccm) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     org.hl7.fhir.r4.model.Enumeration<ConceptMapEquivalence> tgt = new org.hl7.fhir.r4.model.Enumeration<ConceptMapEquivalence>(new org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalenceEnumFactory());
-    ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().copyElement(src, tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
+    ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().copyElement(src, tgt);
-    if (src.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
+    if (ccm.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
-      tgt.setValueAsString(src.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
+      tgt.setValueAsString(ccm.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
     } else {
       switch (src.getValue()) {
         case RELATEDTO:
@@ -306,12 +306,12 @@ public class ConceptMap40_50 {
     return tgt;
   }
 
-  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.r4.model.Enumeration<ConceptMapEquivalence> src) throws FHIRException {
+  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.r4.model.Enumeration<ConceptMapEquivalence> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent tgtCtxt) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     Enumeration<ConceptMapRelationship> tgt = new Enumeration<ConceptMapRelationship>(new Enumerations.ConceptMapRelationshipEnumFactory());
     ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().copyElement(src, tgt);
-    ToolingExtensions.setCodeExtension(tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
+    ToolingExtensions.setCodeExtensionMod(tgtCtxt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
     switch (src.getValue()) {
       case EQUIVALENT:
         tgt.setValue(org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship.EQUIVALENT);

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv43_50/resources43_50/ConceptMap43_50.java

@@ -241,7 +241,7 @@ public class ConceptMap43_50 {
     if (src.hasDisplay())
       tgt.setDisplayElement(String43_50.convertString(src.getDisplayElement()));
     if (src.hasEquivalence())
-      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement()));
+      tgt.setRelationshipElement(convertConceptMapRelationship(src.getEquivalenceElement(), tgt));
     if (src.hasComment())
       tgt.setCommentElement(String43_50.convertString(src.getCommentElement()));
     for (org.hl7.fhir.r4b.model.ConceptMap.OtherElementComponent t : src.getDependsOn())
@@ -255,13 +255,13 @@ public class ConceptMap43_50 {
     if (src == null)
       return null;
     org.hl7.fhir.r4b.model.ConceptMap.TargetElementComponent tgt = new org.hl7.fhir.r4b.model.ConceptMap.TargetElementComponent();
-    ConversionContext43_50.INSTANCE.getVersionConvertor_43_50().copyBackboneElement(src, tgt);
+    ConversionContext43_50.INSTANCE.getVersionConvertor_43_50().copyBackboneElement(src, tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
     if (src.hasCode())
       tgt.setCodeElement(Code43_50.convertCode(src.getCodeElement()));
     if (src.hasDisplay())
       tgt.setDisplayElement(String43_50.convertString(src.getDisplayElement()));
     if (src.hasRelationship())
-      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement()));
+      tgt.setEquivalenceElement(convertConceptMapEquivalence(src.getRelationshipElement(), src));
     else
       tgt.setEquivalence(org.hl7.fhir.r4b.model.ConceptMap.ConceptMapEquivalence.RELATEDTO);
     if (src.hasComment())
@@ -273,13 +273,13 @@ public class ConceptMap43_50 {
     return tgt;
   }
 
-  public static org.hl7.fhir.r4b.model.Enumeration<org.hl7.fhir.r4b.model.ConceptMap.ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src) throws FHIRException {
+  public static org.hl7.fhir.r4b.model.Enumeration<org.hl7.fhir.r4b.model.ConceptMap.ConceptMapEquivalence> convertConceptMapEquivalence(Enumeration<ConceptMapRelationship> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent ccm) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     org.hl7.fhir.r4b.model.Enumeration<org.hl7.fhir.r4b.model.ConceptMap.ConceptMapEquivalence> tgt = new org.hl7.fhir.r4b.model.Enumeration<org.hl7.fhir.r4b.model.ConceptMap.ConceptMapEquivalence>(new org.hl7.fhir.r4b.model.ConceptMap.ConceptMapEquivalenceEnumFactory());
-    ConversionContext43_50.INSTANCE.getVersionConvertor_43_50().copyElement(src, tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
+    ConversionContext43_50.INSTANCE.getVersionConvertor_43_50().copyElement(src, tgt);
-    if (src.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
+    if (ccm.hasExtension(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
-      tgt.setValueAsString(src.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
+      tgt.setValueAsString(ccm.getExtensionString(VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE));
     } else {
       switch (src.getValue()) {
         case RELATEDTO:
@@ -305,12 +305,12 @@ public class ConceptMap43_50 {
     return tgt;
   }
 
-  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.r4b.model.Enumeration<org.hl7.fhir.r4b.model.ConceptMap.ConceptMapEquivalence> src) throws FHIRException {
+  public static Enumeration<ConceptMapRelationship> convertConceptMapRelationship(org.hl7.fhir.r4b.model.Enumeration<org.hl7.fhir.r4b.model.ConceptMap.ConceptMapEquivalence> src, org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent tgtCtxt) throws FHIRException {
     if (src == null || src.isEmpty())
       return null;
     Enumeration<ConceptMapRelationship> tgt = new Enumeration<ConceptMapRelationship>(new Enumerations.ConceptMapRelationshipEnumFactory());
     ConversionContext43_50.INSTANCE.getVersionConvertor_43_50().copyElement(src, tgt);
-    ToolingExtensions.setCodeExtension(tgt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
+    ToolingExtensions.setCodeExtensionMod(tgtCtxt, VersionConvertorConstants.EXT_OLD_CONCEPTMAP_EQUIVALENCE, src.getValueAsString());
     switch (src.getValue()) {
       case EQUIVALENT:
         tgt.setValue(org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship.EQUIVALENT);

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R5ToR5Loader.java

@@ -107,6 +107,13 @@ public class R5ToR5Loader extends BaseLoaderR5 {
     if (patchUrls) {
       doPatchUrls(r5);
     }
+    if (r5 instanceof StructureDefinition) {
+      StructureDefinition sd = (StructureDefinition) r5;
+      if ("http://hl7.org/fhir/StructureDefinition/Base".equals(sd.getUrl())) {
+        sd.getSnapshot().getElementFirstRep().getConstraint().clear();
+        
+      }
+    }
     return r5;
   }
   

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/ToolingExtensions.java

@@ -88,6 +88,8 @@ import org.hl7.fhir.dstu3.model.Type;
 import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.dstu3.model.BackboneElement;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
 
 
@@ -434,6 +436,29 @@ public class ToolingExtensions {
       resource.getExtension().add(new Extension(new UriType(uri)).setValue(new IntegerType(value)));
   }
   
+
+  public static void setCodeExtensionMod(DomainResource resource, String uri, String value) {
+    if (Utilities.noString(value))
+      return;
+
+    Extension ext = getExtension(resource, uri);
+    if (ext != null)
+      ext.setValue(new CodeType(value));
+    else
+      resource.getModifierExtension().add(new Extension(uri).setValue(new CodeType(value)));
+  }
+
+  public static void setCodeExtensionMod(BackboneElement resource, String uri, String value) {
+    if (Utilities.noString(value))
+      return;
+
+    Extension ext = getExtension(resource, uri);
+    if (ext != null)
+      ext.setValue(new CodeType(value));
+    else
+      resource.getModifierExtension().add(new Extension(uri).setValue(new CodeType(value)));
+  }
+
 //  public static String getOID(CodeSystem define) {
 //    return readStringExtension(define, EXT_OID);    
 //  }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/BackboneElement.java

@@ -27,7 +27,7 @@ package org.hl7.fhir.r4.model;
   ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
   POSSIBILITY OF SUCH DAMAGE.
 
-*/
+ */
 
 // Generated on Tue, May 12, 2020 07:26+1000 for FHIR v4.0.1
 import java.util.ArrayList;
@@ -35,6 +35,7 @@ import java.util.List;
 
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
+import org.hl7.fhir.utilities.Utilities;
 
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@@ -277,7 +278,7 @@ public abstract class BackboneElement extends Element implements IBaseBackboneEl
     return super.isEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(modifierExtension);
   }
 
-// added from java-adornments.txt:
+  // added from java-adornments.txt:
 
   public void checkNoModifiers(String noun, String verb) throws FHIRException {
     if (hasModifierExtension()) {
@@ -286,6 +287,119 @@ public abstract class BackboneElement extends Element implements IBaseBackboneEl
 
   }
 
-// end addition
+  public void addModifierExtension(String url, Type value) {
+    if (isDisallowExtensions())
+      throw new Error("Extensions are not allowed in this context");
+    Extension ex = new Extension();
+    ex.setUrl(url);
+    ex.setValue(value);
+    getModifierExtension().add(ex);    
+  }
+
+
+  @Override
+  public Extension getExtensionByUrl(String theUrl) {
+    org.apache.commons.lang3.Validate.notBlank(theUrl, "theUrl must not be blank or null");
+    ArrayList<Extension> retVal = new ArrayList<Extension>();
+    Extension res = super.getExtensionByUrl(theUrl);
+    if (res != null) {
+      retVal.add(res);
+    }
+    for (Extension next : getModifierExtension()) {
+      if (theUrl.equals(next.getUrl())) {
+        retVal.add(next);
+      }
+    }
+    if (retVal.size() == 0)
+      return null;
+    else {
+      org.apache.commons.lang3.Validate.isTrue(retVal.size() == 1, "Url "+theUrl+" must have only one match");
+      return retVal.get(0);
+    }
+  }
+
+  @Override
+  public void removeExtension(String theUrl) {
+    for (int i = getModifierExtension().size()-1; i >= 0; i--) {
+      if (theUrl.equals(getExtension().get(i).getUrl()))
+        getExtension().remove(i);
+    }
+    super.removeExtension(theUrl);
+  }
+
+
+  /**
+   * Returns an unmodifiable list containing all extensions on this element which 
+   * match the given URL.
+   * 
+   * @param theUrl The URL. Must not be blank or null.
+   * @return an unmodifiable list containing all extensions on this element which 
+   * match the given URL
+   */
+  @Override
+  public List<Extension> getExtensionsByUrl(String theUrl) {
+    org.apache.commons.lang3.Validate.notBlank(theUrl, "theUrl must not be blank or null");
+    ArrayList<Extension> retVal = new ArrayList<Extension>();
+    retVal.addAll(super.getExtensionsByUrl(theUrl));
+    for (Extension next : getModifierExtension()) {
+      if (theUrl.equals(next.getUrl())) {
+        retVal.add(next);
+      }
+    }
+    return java.util.Collections.unmodifiableList(retVal);
+  }
+
+  public void copyExtensions(org.hl7.fhir.r4.model.BackboneElement src, String... urls) {
+    super.copyExtensions(src,urls);
+    for (Extension e : src.getModifierExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls)) {
+        addModifierExtension(e.copy());
+      }
+    }    
+  }
+
+  public List<Extension> getExtensionsByUrl(String... theUrls) {
+
+    ArrayList<Extension> retVal = new ArrayList<>();
+    for (Extension next : getModifierExtension()) {
+      if (Utilities.existsInList(next.getUrl(), theUrls)) {
+        retVal.add(next);
+      }
+    }
+    retVal.addAll(super.getExtensionsByUrl(theUrls));
+    return java.util.Collections.unmodifiableList(retVal);
+  }
+
+
+  public boolean hasExtension(String... theUrls) {
+    for (Extension next : getModifierExtension()) {
+      if (Utilities.existsInList(next.getUrl(), theUrls)) {
+        return true;
+      }
+    }
+    return super.hasExtension(theUrls);
+  }
+
+
+  public boolean hasExtension(String theUrl) {
+    for (Extension ext : getModifierExtension()) {
+      if (theUrl.equals(ext.getUrl())) {
+        return true;
+      }
+    }
+
+    return super.hasExtension(theUrl);
+  }
+
+
+  public void copyNewExtensions(org.hl7.fhir.r4.model.BackboneElement src, String... urls) {
+    for (Extension e : src.getModifierExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls) && !!hasExtension(e.getUrl())) {
+        addExtension(e.copy());
+      }
+    }    
+    super.copyNewExtensions(src, urls);
+  }
+  // end addition
 
 }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/BackboneType.java

@@ -27,7 +27,7 @@ package org.hl7.fhir.r4.model;
   ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
   POSSIBILITY OF SUCH DAMAGE.
 
-*/
+ */
 
 // Generated on Mon, Mar 5, 2018 18:26+1100 for FHIR v3.2.0
 import java.util.ArrayList;
@@ -35,6 +35,7 @@ import java.util.List;
 
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
+import org.hl7.fhir.utilities.Utilities;
 
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@@ -267,15 +268,65 @@ public abstract class BackboneType extends Type implements IBaseBackboneElement
     return super.isEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(modifierExtension);
   }
 
-// added from java-adornments.txt:
+  // added from java-adornments.txt:
 
   public void checkNoModifiers(String noun, String verb) throws FHIRException {
     if (hasModifierExtension()) {
       throw new FHIRException("Found unknown Modifier Exceptions on " + noun + " doing " + verb);
     }
-
   }
 
-// end addition
+  public void copyExtensions(org.hl7.fhir.r4.model.BackboneElement src, String... urls) {
+    super.copyExtensions(src,urls);
+    for (Extension e : src.getModifierExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls)) {
+        addModifierExtension(e.copy());
+      }
+    }    
+  }
+
+  public List<Extension> getExtensionsByUrl(String... theUrls) {
+
+    ArrayList<Extension> retVal = new ArrayList<>();
+    for (Extension next : getModifierExtension()) {
+      if (Utilities.existsInList(next.getUrl(), theUrls)) {
+        retVal.add(next);
+      }
+    }
+    retVal.addAll(super.getExtensionsByUrl(theUrls));
+    return java.util.Collections.unmodifiableList(retVal);
+  }
+
+
+  public boolean hasExtension(String... theUrls) {
+    for (Extension next : getModifierExtension()) {
+      if (Utilities.existsInList(next.getUrl(), theUrls)) {
+        return true;
+      }
+    }
+    return super.hasExtension(theUrls);
+  }
+
+
+  public boolean hasExtension(String theUrl) {
+    for (Extension ext : getModifierExtension()) {
+      if (theUrl.equals(ext.getUrl())) {
+        return true;
+      }
+    }
+
+    return super.hasExtension(theUrl);
+  }
+
+
+  public void copyNewExtensions(org.hl7.fhir.r4.model.BackboneElement src, String... urls) {
+    for (Extension e : src.getModifierExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls) && !!hasExtension(e.getUrl())) {
+        addExtension(e.copy());
+      }
+    }    
+    super.copyNewExtensions(src, urls);
+  }
+  // end addition
 
 }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Element.java

@@ -27,7 +27,7 @@ package org.hl7.fhir.r4.model;
   ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
   POSSIBILITY OF SUCH DAMAGE.
 
-*/
+ */
 
 // Generated on Tue, May 12, 2020 07:26+1000 for FHIR v4.0.1
 import java.util.ArrayList;
@@ -36,6 +36,7 @@ import java.util.List;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseElement;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
+import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.utilities.Utilities;
 
 import ca.uhn.fhir.model.api.annotation.Child;
@@ -393,7 +394,7 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
     setId(value);
   }
 
-// added from java-adornments.txt:
+  // added from java-adornments.txt:
   public void addExtension(String url, Type value) {
     if (disallowExtensions)
       throw new Error("Extensions are not allowed in this context");
@@ -446,6 +447,58 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
     return this;
   }
 
-// end addition
+
+  public List<Extension> getExtensionsByUrl(String... theUrls) {
+
+    ArrayList<Extension> retVal = new ArrayList<>();
+    for (Extension next : getExtension()) {
+      if (Utilities.existsInList(next.getUrl(), theUrls)) {
+        retVal.add(next);
+      }
+    }
+    return java.util.Collections.unmodifiableList(retVal);
+  }
+
+
+  public boolean hasExtension(String... theUrls) {
+    for (Extension next : getExtension()) {
+      if (Utilities.existsInList(next.getUrl(), theUrls)) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+
+
+
+  public boolean hasExtension(Extension ext) {
+    if (hasExtension()) {
+      for (Extension t : getExtension()) {
+        if (Base.compareDeep(t, ext, false)) {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  public void copyExtensions(org.hl7.fhir.r4.model.Element src, String... urls) {
+    for (Extension e : src.getExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls)) {
+        addExtension(e.copy());
+      }
+    }    
+  }
+
+  public void copyNewExtensions(org.hl7.fhir.r4.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.r4/src/main/java/org/hl7/fhir/r4/utils/CmdLineApp.java

@@ -10,7 +10,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.context.SimpleWorkerContext;
 import org.hl7.fhir.r4.formats.IParser.OutputStyle;
 import org.hl7.fhir.r4.formats.JsonParser;
-
+import org.hl7.fhir.r4.formats.XmlParser;
 import org.hl7.fhir.r4.model.Base;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Bundle;
@@ -26,6 +26,8 @@ import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.Immunization;
 import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
+import org.hl7.fhir.r4.model.HumanName;
+import org.hl7.fhir.r4.model.Immunization;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Period;
 import org.hl7.fhir.r4.model.Procedure;
@@ -118,7 +120,7 @@ public class CmdLineApp {
         } else if (p.length > 3 && p[0].equals("tx")) {
           tx(p);
         } else {
-          tx(p);
+          System.out.println("Command unknown or not understood: "+cmd);
         }
       } catch (Exception e) {
         System.out.println("Error executing command "+p[0]+": "+e.getMessage());
@@ -170,7 +172,6 @@ public class CmdLineApp {
   }
 
   private void getImmunizations() throws IOException {
-
     Bundle bnd = client.search("Immunization", "?patient="+currentId);
     System.out.println(""+bnd.getTotal()+" Immunizations found. Printing "+bnd.getEntry().size());
     

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/ToolingExtensions.java

@@ -92,6 +92,7 @@ import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.UrlType;
 import org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent;
 import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.r4.model.BackboneElement;
 import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@@ -551,6 +552,30 @@ public class ToolingExtensions {
       element.getExtension().add(new Extension(new UriType(uri)).setValue(new CodeType(value)));
   }
   
+
+  public static void setCodeExtensionMod(DomainResource resource, String uri, String value) {
+    if (Utilities.noString(value))
+      return;
+
+    Extension ext = getExtension(resource, uri);
+    if (ext != null)
+      ext.setValue(new CodeType(value));
+    else
+      resource.getModifierExtension().add(new Extension(uri).setValue(new CodeType(value)));
+  }
+
+  public static void setCodeExtensionMod(BackboneElement resource, String uri, String value) {
+    if (Utilities.noString(value))
+      return;
+
+    Extension ext = getExtension(resource, uri);
+    if (ext != null)
+      ext.setValue(new CodeType(value));
+    else
+      resource.getModifierExtension().add(new Extension(uri).setValue(new CodeType(value)));
+  }
+  
+
   public static void setIntegerExtension(DomainResource resource, String uri, int value) {
     Extension ext = getExtension(resource, uri);
     if (ext != null)

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/model/BackboneElement.java

@@ -34,6 +34,7 @@ import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import org.hl7.fhir.r4b.model.Enumerations.*;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.ICompositeType;
@@ -349,6 +350,57 @@ public abstract class BackboneElement extends DataType implements IBaseBackboneE
     return java.util.Collections.unmodifiableList(retVal);
   }
    
+   public void copyExtensions(org.hl7.fhir.r4b.model.BackboneElement src, String... urls) {
+     super.copyExtensions(src,urls);
+     for (Extension e : src.getModifierExtension()) {
+       if (Utilities.existsInList(e.getUrl(), urls)) {
+         addModifierExtension(e.copy());
+       }
+     }    
+   }
+
+   public List<Extension> getExtensionsByUrl(String... theUrls) {
+
+     ArrayList<Extension> retVal = new ArrayList<>();
+     for (Extension next : getModifierExtension()) {
+       if (Utilities.existsInList(next.getUrl(), theUrls)) {
+         retVal.add(next);
+       }
+     }
+     retVal.addAll(super.getExtensionsByUrl(theUrls));
+     return java.util.Collections.unmodifiableList(retVal);
+   }
+   
+
+   public boolean hasExtension(String... theUrls) {
+     for (Extension next : getModifierExtension()) {
+       if (Utilities.existsInList(next.getUrl(), theUrls)) {
+         return true;
+       }
+     }
+     return super.hasExtension(theUrls);
+   }
+
+
+   public boolean hasExtension(String theUrl) {
+     for (Extension ext : getModifierExtension()) {
+       if (theUrl.equals(ext.getUrl())) {
+         return true;
+       }
+     }
+
+     return super.hasExtension(theUrl);
+   }
+
+
+   public void copyNewExtensions(org.hl7.fhir.r4b.model.BackboneElement src, String... urls) {
+     for (Extension e : src.getModifierExtension()) {
+       if (Utilities.existsInList(e.getUrl(), urls) && !!hasExtension(e.getUrl())) {
+         addExtension(e.copy());
+       }
+     }    
+     super.copyNewExtensions(src, urls);
+   }
 // end addition
 
 }

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/model/BackboneType.java

@@ -34,6 +34,7 @@ import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import org.hl7.fhir.r4b.model.Enumerations.*;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.ICompositeType;
@@ -288,6 +289,58 @@ public abstract class BackboneType extends DataType implements IBaseBackboneElem
     }
 
   }
+
+   public void copyExtensions(org.hl7.fhir.r4b.model.BackboneElement src, String... urls) {
+     super.copyExtensions(src,urls);
+     for (Extension e : src.getModifierExtension()) {
+       if (Utilities.existsInList(e.getUrl(), urls)) {
+         addModifierExtension(e.copy());
+       }
+     }    
+   }
+
+   public List<Extension> getExtensionsByUrl(String... theUrls) {
+
+     ArrayList<Extension> retVal = new ArrayList<>();
+     for (Extension next : getModifierExtension()) {
+       if (Utilities.existsInList(next.getUrl(), theUrls)) {
+         retVal.add(next);
+       }
+     }
+     retVal.addAll(super.getExtensionsByUrl(theUrls));
+     return java.util.Collections.unmodifiableList(retVal);
+   }
+   
+
+   public boolean hasExtension(String... theUrls) {
+     for (Extension next : getModifierExtension()) {
+       if (Utilities.existsInList(next.getUrl(), theUrls)) {
+         return true;
+       }
+     }
+     return super.hasExtension(theUrls);
+   }
+
+
+   public boolean hasExtension(String theUrl) {
+     for (Extension ext : getModifierExtension()) {
+       if (theUrl.equals(ext.getUrl())) {
+         return true;
+       }
+     }
+
+     return super.hasExtension(theUrl);
+   }
+
+
+   public void copyNewExtensions(org.hl7.fhir.r4b.model.BackboneElement src, String... urls) {
+     for (Extension e : src.getModifierExtension()) {
+       if (Utilities.existsInList(e.getUrl(), urls) && !!hasExtension(e.getUrl())) {
+         addExtension(e.copy());
+       }
+     }    
+     super.copyNewExtensions(src, urls);
+   }
 // end addition
 
 }

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/model/Element.java

@@ -445,12 +445,15 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
     * Note: BackbdoneElements override this to add matching Modifier Extensions too
     * 
     * @param theUrl The URL. Must not be blank or null.
-   * @return an unmodifiable list containing all extensions on this element which
+    * @return an unmodifiable list containing all extensions on this element which match the given URL
-   *         match the given URL
     */
    public List<Extension> getExtensionsByUrl(String theUrl) {
-    org.apache.commons.lang3.Validate.notBlank(theUrl, "theUrl must not be blank or null");
+     if (theUrl == null) {
-    ArrayList<Extension> retVal = new ArrayList<Extension>();
+       throw new NullPointerException("theUrl must not be null");
+     } else if (theUrl.length() == 0) {
+       throw new IllegalArgumentException("theUrl must not be empty");
+     }
+     ArrayList<Extension> retVal = new ArrayList<>();
      for (Extension next : getExtension()) {
        if (theUrl.equals(next.getUrl())) {
          retVal.add(next);
@@ -459,6 +462,28 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
      return java.util.Collections.unmodifiableList(retVal);
    }
    
+   public List<Extension> getExtensionsByUrl(String... theUrls) {
+     
+     ArrayList<Extension> retVal = new ArrayList<>();
+     for (Extension next : getExtension()) {
+       if (Utilities.existsInList(next.getUrl(), theUrls)) {
+         retVal.add(next);
+       }
+     }
+     return java.util.Collections.unmodifiableList(retVal);
+   }
+   
+
+   public boolean hasExtension(String... theUrls) {
+     for (Extension next : getExtension()) {
+       if (Utilities.existsInList(next.getUrl(), theUrls)) {
+         return true;
+       }
+     }
+     return false;
+   }
+
+
    /**
     * Returns an true if this element has an extension that matchs the given URL.
     * 
@@ -467,12 +492,21 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
     * @param theUrl The URL. Must not be blank or null.
     */
    public boolean hasExtension(String theUrl) {
-    return !getExtensionsByUrl(theUrl).isEmpty();
+     if (extension == null || extension.size() == 0) {
+       return false;
+     }
+
+     for (Extension ext : extension) {
+       if (theUrl.equals(ext.getUrl())) {
+         return true;
+       }
+     }
+
+     return false;
    }
 
    /**
-   * Returns the value as a string if this element has only one extension that
+    * Returns the value as a string if this element has only one extension that matches the given URL, and that can be converted to a string.
-   * matches the given URL, and that can be converted to a string.
     * 
     * Note: BackbdoneElements override this to check Modifier Extensions too
     * 
@@ -483,12 +517,42 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
     if (ext.isEmpty()) 
       return null; 
     if (ext.size() > 1) 
-      throw new FHIRException("Multiple matching extensions found");
+      throw new FHIRException("Multiple matching extensions found for extension '"+theUrl+"'");
+    if (!ext.get(0).hasValue())
+      return null;
     if (!ext.get(0).getValue().isPrimitive())
-      throw new FHIRException("Extension could not be converted to a string");
+      throw new FHIRException("Extension '"+theUrl+"' could not be converted to a string");
     return ext.get(0).getValue().primitiveValue();
   }
 
+
+  public boolean hasExtension(Extension ext) {
+    if (hasExtension()) {
+      for (Extension t : getExtension()) {
+        if (Base.compareDeep(t, ext, false)) {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+  
+  public void copyExtensions(org.hl7.fhir.r4b.model.Element src, String... urls) {
+    for (Extension e : src.getExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls)) {
+        addExtension(e.copy());
+      }
+    }    
+  }
+
+  public void copyNewExtensions(org.hl7.fhir.r4b.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.r4b/src/main/java/org/hl7/fhir/r4b/utils/ToolingExtensions.java

@@ -97,6 +97,7 @@ import org.hl7.fhir.r4b.model.UriType;
 import org.hl7.fhir.r4b.model.UrlType;
 import org.hl7.fhir.r4b.model.ValueSet.ConceptReferenceComponent;
 import org.hl7.fhir.r4b.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.r4b.model.BackboneElement;
 import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@@ -106,8 +107,8 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
 public class ToolingExtensions {
 
   // validated
-//  private static final String EXT_OID = "http://hl7.org/fhir/StructureDefinition/valueset-oid";
+  //  private static final String EXT_OID = "http://hl7.org/fhir/StructureDefinition/valueset-oid";
-//  public static final String EXT_DEPRECATED = "http://hl7.org/fhir/StructureDefinition/codesystem-deprecated";
+  //  public static final String EXT_DEPRECATED = "http://hl7.org/fhir/StructureDefinition/codesystem-deprecated";
   public static final String EXT_DEFINITION = "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition";
   public static final String EXT_CS_COMMENT = "http://hl7.org/fhir/StructureDefinition/codesystem-concept-comments";
   public static final String EXT_VS_COMMENT = "http://hl7.org/fhir/StructureDefinition/valueset-concept-comments";
@@ -134,12 +135,12 @@ public class ToolingExtensions {
   public static final String EXT_MAPPING_PREFIX = "http://hl7.org/fhir/tools/StructureDefinition/logical-mapping-prefix";
   public static final String EXT_MAPPING_SUFFIX = "http://hl7.org/fhir/tools/StructureDefinition/logical-mapping-suffix";
 
-//  public static final String EXT_FLYOVER = "http://hl7.org/fhir/Profile/questionnaire-extensions#flyover";
+  //  public static final String EXT_FLYOVER = "http://hl7.org/fhir/Profile/questionnaire-extensions#flyover";
   public static final String EXT_QTYPE = "http://hl7.org/fhir/StructureDefinition/questionnnaire-baseType";
-//  private static final String EXT_QREF = "http://www.healthintersections.com.au/fhir/Profile/metadata#reference";
+  //  private static final String EXT_QREF = "http://www.healthintersections.com.au/fhir/Profile/metadata#reference";
-//  private static final String EXTENSION_FILTER_ONLY = "http://www.healthintersections.com.au/fhir/Profile/metadata#expandNeedsFilter";
+  //  private static final String EXTENSION_FILTER_ONLY = "http://www.healthintersections.com.au/fhir/Profile/metadata#expandNeedsFilter";
-//  private static final String EXT_TYPE = "http://www.healthintersections.com.au/fhir/Profile/metadata#type";
+  //  private static final String EXT_TYPE = "http://www.healthintersections.com.au/fhir/Profile/metadata#type";
-//  private static final String EXT_REFERENCE = "http://www.healthintersections.com.au/fhir/Profile/metadata#reference";
+  //  private static final String EXT_REFERENCE = "http://www.healthintersections.com.au/fhir/Profile/metadata#reference";
   private static final String EXT_FHIRTYPE = "http://hl7.org/fhir/StructureDefinition/questionnaire-fhirType";
   private static final String EXT_ALLOWABLE_UNITS = "http://hl7.org/fhir/StructureDefinition/elementdefinition-allowedUnits";
   public static final String EXT_CIMI_REFERENCE = "http://hl7.org/fhir/StructureDefinition/cimi-reference";
@@ -166,8 +167,8 @@ public class ToolingExtensions {
   public static final String EXT_IGP_MAPPING_CSV = "http://hl7.org/fhir/StructureDefinition/igpublisher-mapping-csv";
   public static final String EXT_IGP_BUNDLE = "http://hl7.org/fhir/StructureDefinition/igpublisher-bundle";
   public static final String EXT_IGP_RESOURCE_INFO = "http://hl7.org/fhir/tools/StructureDefinition/resource-information";
-//  public static final String EXT_IGP_CONTAINED_RESOURCE_INFO = "http://hl7.org/fhir/tools/StructureDefinition/contained-resource-information";
+  //  public static final String EXT_IGP_CONTAINED_RESOURCE_INFO = "http://hl7.org/fhir/tools/StructureDefinition/contained-resource-information";
-//  public static final String EXT_IGP_LOADVERSION = "http://hl7.org/fhir/StructureDefinition/igpublisher-loadversion";
+  //  public static final String EXT_IGP_LOADVERSION = "http://hl7.org/fhir/StructureDefinition/igpublisher-loadversion";
   public static final String EXT_MAX_VALUESET = "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet";
   public static final String EXT_MIN_VALUESET = "http://hl7.org/fhir/StructureDefinition/elementdefinition-minValueSet";
   public static final String EXT_PROFILE_ELEMENT = "http://hl7.org/fhir/StructureDefinition/elementdefinition-profile-element";
@@ -182,7 +183,7 @@ public class ToolingExtensions {
   public static final String EXT_FHIR_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type";
   public static final String EXT_XML_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type";
   public static final String EXT_RENDERED_VALUE = "http://hl7.org/fhir/StructureDefinition/rendered-value";
-  public static final String EXT_OLD_CONCEPTMAP_EQUIVALENCE = "http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.element.target.equivalence";
+  public static final String EXT_OLD_CONCEPTMAP_EQUIVALENCE = "http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.group.element.target.equivalence";
   public static final String EXT_EXP_TOOCOSTLY = "http://hl7.org/fhir/StructureDefinition/valueset-toocostly";
   public static final String EXT_MUST_SUPPORT = "http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support";
   public static final String EXT_TRANSLATABLE = "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable";
@@ -223,15 +224,15 @@ public class ToolingExtensions {
     return getExtension(e, url) != null;
   }
 
-//  public static void addStringExtension(DomainResource dr, String url, String content) {
+  //  public static void addStringExtension(DomainResource dr, String url, String content) {
-//    if (!StringUtils.isBlank(content)) {
+  //    if (!StringUtils.isBlank(content)) {
-//      Extension ex = getExtension(dr, url);
+  //      Extension ex = getExtension(dr, url);
-//      if (ex != null)
+  //      if (ex != null)
-//        ex.setValue(new StringType(content));
+  //        ex.setValue(new StringType(content));
-//      else
+  //      else
-//        dr.getExtension().add(Factory.newExtension(url, new StringType(content), true));   
+  //        dr.getExtension().add(Factory.newExtension(url, new StringType(content), true));   
-//    }
+  //    }
-//  }
+  //  }
 
   public static void addMarkdownExtension(DomainResource dr, String url, String content) {
     if (!StringUtils.isBlank(content)) {
@@ -320,10 +321,10 @@ public class ToolingExtensions {
       nc.getExtension().add(Factory.newExtension(EXT_CS_COMMENT, Factory.newString_(comment), true));
   }
 
-//  public static void markDeprecated(Element nc) {
+  //  public static void markDeprecated(Element nc) {
-//    setDeprecated(nc);   
+  //    setDeprecated(nc);   
-//  }
+  //  }
-//
+  //
 
   public static void addDefinition(Element nc, String definition) {
     if (!StringUtils.isBlank(definition))
@@ -459,18 +460,18 @@ public class ToolingExtensions {
   public static String getCSComment(ConceptDefinitionComponent c) {
     return readStringExtension(c, EXT_CS_COMMENT);
   }
-//
+  //
-//  public static Boolean getDeprecated(Element c) {
+  //  public static Boolean getDeprecated(Element c) {
-//    return readBooleanExtension(c, EXT_DEPRECATED);    
+  //    return readBooleanExtension(c, EXT_DEPRECATED);    
-//  }
+  //  }
 
   public static boolean hasCSComment(ConceptDefinitionComponent c) {
     return findStringExtension(c, EXT_CS_COMMENT);
   }
 
-//  public static boolean hasDeprecated(Element c) {
+  //  public static boolean hasDeprecated(Element c) {
-//    return findBooleanExtension(c, EXT_DEPRECATED);    
+  //    return findBooleanExtension(c, EXT_DEPRECATED);    
-//  }
+  //  }
 
   public static void addFlyOver(QuestionnaireItemComponent item, String text, String linkId) {
     if (!StringUtils.isBlank(text)) {
@@ -582,6 +583,28 @@ public class ToolingExtensions {
       element.getExtension().add(new Extension(uri).setValue(new CodeType(value)));
   }
 
+  public static void setCodeExtensionMod(DomainResource resource, String uri, String value) {
+    if (Utilities.noString(value))
+      return;
+
+    Extension ext = getExtension(resource, uri);
+    if (ext != null)
+      ext.setValue(new CodeType(value));
+    else
+      resource.getModifierExtension().add(new Extension(uri).setValue(new CodeType(value)));
+  }
+
+  public static void setCodeExtensionMod(BackboneElement resource, String uri, String value) {
+    if (Utilities.noString(value))
+      return;
+
+    Extension ext = getExtension(resource, uri);
+    if (ext != null)
+      ext.setValue(new CodeType(value));
+    else
+      resource.getModifierExtension().add(new Extension(uri).setValue(new CodeType(value)));
+  }
+
   public static void setIntegerExtension(DomainResource resource, String uri, int value) {
     Extension ext = getExtension(resource, uri);
     if (ext != null)
@@ -590,34 +613,34 @@ public class ToolingExtensions {
       resource.getExtension().add(new Extension(uri).setValue(new IntegerType(value)));
   }
 
-//  public static String getOID(CodeSystem define) {
+  //  public static String getOID(CodeSystem define) {
-//    return readStringExtension(define, EXT_OID);    
+  //    return readStringExtension(define, EXT_OID);    
-//  }
+  //  }
-//
+  //
-//  public static String getOID(ValueSet vs) {
+  //  public static String getOID(ValueSet vs) {
-//    return readStringExtension(vs, EXT_OID);    
+  //    return readStringExtension(vs, EXT_OID);    
-//  }
+  //  }
-//
+  //
-//  public static void setOID(CodeSystem define, String oid) throws FHIRFormatError, URISyntaxException {
+  //  public static void setOID(CodeSystem define, String oid) throws FHIRFormatError, URISyntaxException {
-//    if (!oid.startsWith("urn:oid:"))
+  //    if (!oid.startsWith("urn:oid:"))
-//      throw new FHIRFormatError("Error in OID format");
+  //      throw new FHIRFormatError("Error in OID format");
-//    if (oid.startsWith("urn:oid:urn:oid:"))
+  //    if (oid.startsWith("urn:oid:urn:oid:"))
-//      throw new FHIRFormatError("Error in OID format");
+  //      throw new FHIRFormatError("Error in OID format");
-//    if (!hasExtension(define, EXT_OID))
+  //    if (!hasExtension(define, EXT_OID))
-//    define.getExtension().add(Factory.newExtension(EXT_OID, Factory.newUri(oid), false));       
+  //    define.getExtension().add(Factory.newExtension(EXT_OID, Factory.newUri(oid), false));       
-//    else if (!oid.equals(readStringExtension(define, EXT_OID)))
+  //    else if (!oid.equals(readStringExtension(define, EXT_OID)))
-//      throw new Error("Attempt to assign multiple OIDs to a code system");
+  //      throw new Error("Attempt to assign multiple OIDs to a code system");
-//  }
+  //  }
-//  public static void setOID(ValueSet vs, String oid) throws FHIRFormatError, URISyntaxException {
+  //  public static void setOID(ValueSet vs, String oid) throws FHIRFormatError, URISyntaxException {
-//    if (!oid.startsWith("urn:oid:"))
+  //    if (!oid.startsWith("urn:oid:"))
-//      throw new FHIRFormatError("Error in OID format");
+  //      throw new FHIRFormatError("Error in OID format");
-//    if (oid.startsWith("urn:oid:urn:oid:"))
+  //    if (oid.startsWith("urn:oid:urn:oid:"))
-//      throw new FHIRFormatError("Error in OID format");
+  //      throw new FHIRFormatError("Error in OID format");
-//    if (!hasExtension(vs, EXT_OID))
+  //    if (!hasExtension(vs, EXT_OID))
-//    vs.getExtension().add(Factory.newExtension(EXT_OID, Factory.newUri(oid), false));       
+  //    vs.getExtension().add(Factory.newExtension(EXT_OID, Factory.newUri(oid), false));       
-//    else if (!oid.equals(readStringExtension(vs, EXT_OID)))
+  //    else if (!oid.equals(readStringExtension(vs, EXT_OID)))
-//      throw new Error("Attempt to assign multiple OIDs to value set "+vs.getName()+" ("+vs.getUrl()+"). Has "+readStringExtension(vs, EXT_OID)+", trying to add "+oid);
+  //      throw new Error("Attempt to assign multiple OIDs to value set "+vs.getName()+" ("+vs.getUrl()+"). Has "+readStringExtension(vs, EXT_OID)+", trying to add "+oid);
-//  }
+  //  }
 
   public static boolean hasLanguageTranslation(Element element, String lang) {
     for (Extension e : element.getExtension()) {
@@ -687,23 +710,23 @@ public class ToolingExtensions {
     return results;
   }
 
-//  public static void addDEReference(DataElement de, String value) {
+  //  public static void addDEReference(DataElement de, String value) {
-//    for (Extension e : de.getExtension()) 
+  //    for (Extension e : de.getExtension()) 
-//      if (e.getUrl().equals(EXT_CIMI_REFERENCE)) {
+  //      if (e.getUrl().equals(EXT_CIMI_REFERENCE)) {
-//        e.setValue(new UriType(value));
+  //        e.setValue(new UriType(value));
-//        return;
+  //        return;
-//      }
+  //      }
-//    de.getExtension().add(new Extension().setUrl(EXT_CIMI_REFERENCE).setValue(new UriType(value)));
+  //    de.getExtension().add(new Extension().setUrl(EXT_CIMI_REFERENCE).setValue(new UriType(value)));
-//  }
+  //  }
 
-//  public static void setDeprecated(Element nc) {
+  //  public static void setDeprecated(Element nc) {
-//    for (Extension e : nc.getExtension()) 
+  //    for (Extension e : nc.getExtension()) 
-//      if (e.getUrl().equals(EXT_DEPRECATED)) {
+  //      if (e.getUrl().equals(EXT_DEPRECATED)) {
-//        e.setValue(new BooleanType(true));
+  //        e.setValue(new BooleanType(true));
-//        return;
+  //        return;
-//      }
+  //      }
-//    nc.getExtension().add(new Extension().setUrl(EXT_DEPRECATED).setValue(new BooleanType(true)));    
+  //    nc.getExtension().add(new Extension().setUrl(EXT_DEPRECATED).setValue(new BooleanType(true)));    
-//  }
+  //  }
 
   public static void setExtension(Element focus, String url, Coding c) {
     for (Extension e : focus.getExtension())
@@ -908,14 +931,14 @@ public class ToolingExtensions {
     return type.primitiveValue();
   }
 
-//  public static boolean hasOID(ValueSet vs) {
+  //  public static boolean hasOID(ValueSet vs) {
-//    return hasExtension(vs, EXT_OID);
+  //    return hasExtension(vs, EXT_OID);
-//  }
+  //  }
-//  
+  //  
-//  public static boolean hasOID(CodeSystem cs) {
+  //  public static boolean hasOID(CodeSystem cs) {
-//    return hasExtension(cs, EXT_OID);
+  //    return hasExtension(cs, EXT_OID);
-//  }
+  //  }
-//  
+  //  
   public static void addUrlExtension(Element e, String url, String content) {
     if (!StringUtils.isBlank(content)) {
       Extension ex = getExtension(e, url);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/StructureDefinitionHacker.java

@@ -8,7 +8,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.utilities.VersionUtilities;
 
 /**
- * This doesn't do anythign at this time
+ * This works around known issues in struture definitions
  * 
  * @author graha
  *

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

@@ -2472,7 +2472,30 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
         return res;
       }
     } 
-    return typeManager.fetchTypeDefinition(typeName);
+    StructureDefinition p = typeManager.fetchTypeDefinition(typeName);
+    if (p != null && !p.isGeneratedSnapshot()) {
+      if (p.isGeneratingSnapshot()) {
+        throw new FHIRException("Attempt to fetch the profile "+p.getVersionedUrl()+" while generating the snapshot for it");
+      }
+      try {
+        if (logger.isDebugLogging()) {
+          System.out.println("Generating snapshot for "+p.getVersionedUrl());
+        }
+        p.setGeneratingSnapshot(true);
+        try {
+          new ContextUtilities(this).generateSnapshot(p);
+        } finally {
+          p.setGeneratingSnapshot(false);      
+        }
+      } catch (Exception e) {
+        // not sure what to do in this case?
+        System.out.println("Unable to generate snapshot @4 for "+p.getVersionedUrl()+": "+e.getMessage());
+        if (logger.isDebugLogging()) {
+          e.printStackTrace();
+        }
+      }
+    }
+    return p;
   }
   
   @Override

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Manager.java

@@ -95,6 +95,9 @@ public class Manager {
       return null;
     }
     public static FhirFormat readFromMimeType(String mt) {
+      if (mt == null) {
+        return null;
+      }
       if (mt.contains("/xml") || mt.contains("+xml")) {
         return FhirFormat.XML;
       }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ParserBase.java

@@ -49,6 +49,7 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
+import org.hl7.fhir.utilities.validation.IDigitalSignatureServices;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
@@ -86,6 +87,7 @@ public abstract class ParserBase {
   protected boolean showDecorations;
   protected IdRenderingPolicy idPolicy = IdRenderingPolicy.All;
   protected StructureDefinition logical;
+  protected IDigitalSignatureServices signatureServices;
   
 	public ParserBase(IWorkerContext context) {
 		super();
@@ -281,4 +283,12 @@ public abstract class ParserBase {
     return this;
   }
 
+  public IDigitalSignatureServices getSignatureServices() {
+    return signatureServices;
+  }
+
+  public void setSignatureServices(IDigitalSignatureServices signatureServices) {
+    this.signatureServices = signatureServices;
+  }
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/SHCParser.java

@@ -329,7 +329,7 @@ public class SHCParser extends ParserBase {
       String url = Utilities.pathURL(iss, "/.well-known/jwks.json");
       JsonObject jwks = null;
       try {
-        jwks = org.hl7.fhir.utilities.json.parser.JsonParser.parseObjectFromUrl(url);
+        jwks = signatureServices != null ? signatureServices.fetchJWKS(url) : org.hl7.fhir.utilities.json.parser.JsonParser.parseObjectFromUrl(url);
       } catch (Exception e) {
         logError(errors, "2023-09-08", 1, 1, name, IssueType.NOTFOUND, "Unable to verify the signature, because unable to retrieve JWKS from "+url+": "+
            e.getMessage().replace("Connection refused (Connection refused)", "Connection refused"), IssueSeverity.ERROR);    

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java

@@ -326,8 +326,7 @@ public class XmlParser extends ParserBase {
           n.setPath(element.getPath()+"."+property.getName());
           element.getChildren().add(n);
         }
-      } 
+      } else {
-      else {
         Node n = node.getFirstChild();
         while (n != null) {
           if (n.getNodeType() == Node.TEXT_NODE && !Utilities.noString(n.getTextContent().trim())) {

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

@@ -323,7 +323,48 @@ Modifier extensions SHALL NOT change the meaning of any elements on Resource or
      }    
    }
 
+   public List<Extension> getExtensionsByUrl(String... theUrls) {
 
+     ArrayList<Extension> retVal = new ArrayList<>();
+     for (Extension next : getModifierExtension()) {
+       if (Utilities.existsInList(next.getUrl(), theUrls)) {
+         retVal.add(next);
+       }
+     }
+     retVal.addAll(super.getExtensionsByUrl(theUrls));
+     return java.util.Collections.unmodifiableList(retVal);
+   }
+   
+
+   public boolean hasExtension(String... theUrls) {
+     for (Extension next : getModifierExtension()) {
+       if (Utilities.existsInList(next.getUrl(), theUrls)) {
+         return true;
+       }
+     }
+     return super.hasExtension(theUrls);
+   }
+
+
+   public boolean hasExtension(String theUrl) {
+     for (Extension ext : getModifierExtension()) {
+       if (theUrl.equals(ext.getUrl())) {
+         return true;
+       }
+     }
+
+     return super.hasExtension(theUrl);
+   }
+
+
+   public void copyNewExtensions(org.hl7.fhir.r5.model.BackboneElement src, String... urls) {
+     for (Extension e : src.getModifierExtension()) {
+       if (Utilities.existsInList(e.getUrl(), urls) && !!hasExtension(e.getUrl())) {
+         addExtension(e.copy());
+       }
+     }    
+     super.copyNewExtensions(src, urls);
+   }
 
 // end addition
 

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

@@ -35,6 +35,7 @@ import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import org.hl7.fhir.r5.model.Enumerations.*;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.ICompositeType;
@@ -243,14 +244,67 @@ Modifier extensions SHALL NOT change the meaning of any elements on Resource or
     return super.isEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(modifierExtension);
   }
 
-// Manual code (from Configuration.txt):
+  // Manual code (from Configuration.txt):
-public void checkNoModifiers(String noun, String verb) throws FHIRException {
+  public void checkNoModifiers(String noun, String verb) throws FHIRException {
     if (hasModifierExtension()) {
       throw new FHIRException("Found unknown Modifier Exceptions on "+noun+" doing "+verb);
     }
 
   }
-// end addition
+
+
+  public void copyExtensions(org.hl7.fhir.r5.model.BackboneElement src, String... urls) {
+    super.copyExtensions(src,urls);
+    for (Extension e : src.getModifierExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls)) {
+        addModifierExtension(e.copy());
+      }
+    }    
+  }
+
+  public List<Extension> getExtensionsByUrl(String... theUrls) {
+
+    ArrayList<Extension> retVal = new ArrayList<>();
+    for (Extension next : getModifierExtension()) {
+      if (Utilities.existsInList(next.getUrl(), theUrls)) {
+        retVal.add(next);
+      }
+    }
+    retVal.addAll(super.getExtensionsByUrl(theUrls));
+    return java.util.Collections.unmodifiableList(retVal);
+  }
+
+
+  public boolean hasExtension(String... theUrls) {
+    for (Extension next : getModifierExtension()) {
+      if (Utilities.existsInList(next.getUrl(), theUrls)) {
+        return true;
+      }
+    }
+    return super.hasExtension(theUrls);
+  }
+
+
+  public boolean hasExtension(String theUrl) {
+    for (Extension ext : getModifierExtension()) {
+      if (theUrl.equals(ext.getUrl())) {
+        return true;
+      }
+    }
+
+    return super.hasExtension(theUrl);
+  }
+
+
+  public void copyNewExtensions(org.hl7.fhir.r5.model.BackboneElement src, String... urls) {
+    for (Extension e : src.getModifierExtension()) {
+      if (Utilities.existsInList(e.getUrl(), urls) && !!hasExtension(e.getUrl())) {
+        addExtension(e.copy());
+      }
+    }    
+    super.copyNewExtensions(src, urls);
+  }
+  // end addition
 
 }
 

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

@@ -132,6 +132,7 @@ public class TypeDetails {
   private List<ProfiledType> types = new ArrayList<ProfiledType>();
   private CollectionStatus collectionStatus;
   private Set<String> targets; // or, not and, canonical urls
+  private boolean choice;
 
   public TypeDetails(CollectionStatus collectionStatus, String... names) {
     super();
@@ -308,6 +309,9 @@ public class TypeDetails {
       }
       targets.addAll(source.targets);
     }
+    if (source.isChoice()) {
+      choice = true;
+    }
   }
   
   public TypeDetails union(TypeDetails right) {
@@ -537,4 +541,12 @@ public class TypeDetails {
     return collectionStatus != null && collectionStatus.isList();
   }
   
+  // for SQL-on-FHIR: warnings when .ofType() is not paired with a choice element
+  public void setChoice(boolean b) {
+    choice = true;
+  }
+  public boolean isChoice() {
+    return choice;
+  }
+  
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ConceptMapRenderer.java

@@ -169,8 +169,8 @@ public class ConceptMapRenderer extends TerminologyRenderer {
             if (!ccm.hasRelationship())
               tr.td().tx(":"+"("+ConceptMapRelationship.EQUIVALENT.toCode()+")");
             else {
-              if (ccm.getRelationshipElement().hasExtension(ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
+              if (ccm.hasExtension(ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
-                String code = ToolingExtensions.readStringExtension(ccm.getRelationshipElement(), ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
+                String code = ToolingExtensions.readStringExtension(ccm, ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
                 tr.td().ah(eqpath+"#"+code, code).tx(presentEquivalenceCode(code));                
               } else {
                 tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode(), ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/StructureDefinitionRenderer.java

@@ -848,8 +848,16 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
       if (element.hasSliceName())
         sName = sName +":"+element.getSliceName();
       used.used = true;
-      if (logicalModel && element.hasRepresentation(PropertyRepresentation.XMLATTR))
+      if (logicalModel) {
+        if (element.hasRepresentation(PropertyRepresentation.XMLATTR)) {
           sName = "@"+sName;
+        } else if (element.hasUserData("derived.pointer")) {
+          ElementDefinition drv = (ElementDefinition) element.getUserData("derived.pointer");
+          if (drv.hasRepresentation(PropertyRepresentation.XMLATTR)) {
+            sName = "@"+sName;
+          }
+        }
+      }
       Cell nc = genElementNameCell(gen, element, profileBaseFileName, snapshot, corePath, imagePath, root, logicalModel, allInvariants, profile, typesRow, row, hasDef, ext, used, ref, sName, all);
       switch (context.getStructureMode()) {
       case BINDINGS:

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

@@ -135,6 +135,7 @@ public class FHIRPathEngine {
   private boolean doNotEnforceAsCaseSensitive;
   private boolean allowDoubleQuotes;
   private List<String> typeWarnings = new ArrayList<>();
+  private boolean emitSQLonFHIRWarning;
 
   // if the fhir path expressions are allowed to use constants beyond those defined in the specification
   // the application can implement them by providing a constant resolver 
@@ -474,7 +475,7 @@ public class FHIRPathEngine {
       }
     }
 
-    return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, elementDependencies, true, false);
+    return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, elementDependencies, true, false, expr);
   }
   
   /**
@@ -531,14 +532,14 @@ public class FHIRPathEngine {
         }
       }
     }
-    TypeDetails res = executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, null, true, false);
+    TypeDetails res = executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, null, true, false, expr);
     warnings.addAll(typeWarnings);
     return res;
   }
   
   public TypeDetails checkOnTypes(Object appContext, String resourceType, TypeDetails types, ExpressionNode expr, List<String> warnings) throws FHIRLexerException, PathEngineException, DefinitionException {
     typeWarnings.clear();
-    TypeDetails res = executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, null, true, false);
+    TypeDetails res = executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, null, true, false, expr);
     warnings.addAll(typeWarnings);
     return res;
   }
@@ -566,7 +567,7 @@ public class FHIRPathEngine {
       }
     }
 
-    return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, elementDependencies, true, false);
+    return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, elementDependencies, true, false, expr);
   }
 
   private FHIRException makeExceptionPlural(Integer num, ExpressionNode holder, String constName, Object... args) {
@@ -615,13 +616,13 @@ public class FHIRPathEngine {
       }
     }
 
-    return executeType(new ExecutionTypeContext(appContext, sd.getUrl(), types, types), types, expr, null, true, false);
+    return executeType(new ExecutionTypeContext(appContext, sd.getUrl(), types, types), types, expr, null, true, false, expr);
   }
 
   public TypeDetails check(Object appContext, StructureDefinition sd, ExpressionNode expr) throws FHIRLexerException, PathEngineException, DefinitionException {
     // if context is a path that refers to a type, do that conversion now 
     TypeDetails types = null; // this is a special case; the first path reference will have to resolve to something in the context
-    return executeType(new ExecutionTypeContext(appContext, sd == null ? null : sd.getUrl(), null, types), types, expr, null, true, false);
+    return executeType(new ExecutionTypeContext(appContext, sd == null ? null : sd.getUrl(), null, types), types, expr, null, true, false, expr);
   }
 
   public TypeDetails check(Object appContext, String resourceType, String context, String expr) throws FHIRLexerException, PathEngineException, DefinitionException {
@@ -1515,7 +1516,8 @@ public class FHIRPathEngine {
     return new TypeDetails(CollectionStatus.SINGLETON, exp.getName());
   }
 
-  private TypeDetails executeType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, Set<ElementDefinition> elementDependencies, boolean atEntry, boolean canBeNone) throws PathEngineException, DefinitionException {
+  private TypeDetails executeType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, Set<ElementDefinition> elementDependencies, boolean atEntry, boolean canBeNone, ExpressionNode container) throws PathEngineException, DefinitionException {
+    
     TypeDetails result = new TypeDetails(null);
     switch (exp.getKind()) {
     case Name:
@@ -1539,9 +1541,10 @@ public class FHIRPathEngine {
           }
         }
       }
+      doSQLOnFHIRCheck(result, exp);
       break;
     case Function:
-      result.update(evaluateFunctionType(context, focus, exp, elementDependencies));
+      result.update(evaluateFunctionType(context, focus, exp, elementDependencies, container));
       break;
     case Unary:
       result.addType(TypeDetails.FP_Integer);
@@ -1552,12 +1555,12 @@ public class FHIRPathEngine {
       result.update(resolveConstantType(context, exp.getConstant(), exp));
       break;
     case Group:
-      result.update(executeType(context, focus, exp.getGroup(), elementDependencies, atEntry, canBeNone));
+      result.update(executeType(context, focus, exp.getGroup(), elementDependencies, atEntry, canBeNone, exp));
     }
     exp.setTypes(result);
 
     if (exp.getInner() != null) {
-      result = executeType(context, result, exp.getInner(), elementDependencies, false, false);
+      result = executeType(context, result, exp.getInner(), elementDependencies, false, false, exp);
     }
 
     if (exp.isProximal() && exp.getOperation() != null) {
@@ -1568,7 +1571,7 @@ public class FHIRPathEngine {
         if (last.getOperation() == Operation.Is || last.getOperation() == Operation.As) {
           work = executeTypeName(context, focus, next, atEntry);
         } else {
-          work = executeType(context, focus, next, elementDependencies, atEntry, canBeNone);
+          work = executeType(context, focus, next, elementDependencies, atEntry, canBeNone, exp);
         }
         result = operateTypes(result, last.getOperation(), work, last);
         last = next;
@@ -1579,6 +1582,19 @@ public class FHIRPathEngine {
     return result;
   }
 
+  private void doSQLOnFHIRCheck(TypeDetails focus, ExpressionNode expr) {
+    if (emitSQLonFHIRWarning) {
+      // special Logic for SQL-on-FHIR:
+      if (focus.isChoice()) {
+        if (expr.getInner() == null || expr.getInner().getFunction() != Function.OfType) {
+          typeWarnings.add(worker.formatMessage(I18nConstants.FHIRPATH_CHOICE_NO_TYPE_SPECIFIER, expr.toString()));
+        }
+      } else if (expr.getInner() != null && expr.getInner().getFunction() == Function.OfType) {
+        typeWarnings.add(worker.formatMessage(I18nConstants.FHIRPATH_CHOICE_SPURIOUS_TYPE_SPECIFIER, expr.toString()));
+      }
+    }
+  }
+
   private List<Base> resolveConstant(ExecutionContext context, Base constant, boolean beforeContext, ExpressionNode expr) throws PathEngineException {
     if (constant == null) {
       return new ArrayList<Base>();
@@ -3129,16 +3145,16 @@ public class FHIRPathEngine {
     int i = 0;
     for (ExpressionNode expr : exp.getParameters()) {
       if (isExpressionParameter(exp, i)) {
-        paramTypes.add(executeType(changeThis(context, focus), focus, expr, elementDependencies, true, canBeNone));
+        paramTypes.add(executeType(changeThis(context, focus), focus, expr, elementDependencies, true, canBeNone, expr));
       } else {
-        paramTypes.add(executeType(context, context.thisItem, expr, elementDependencies, true, canBeNone));
+        paramTypes.add(executeType(context, context.thisItem, expr, elementDependencies, true, canBeNone, expr));
       }
       i++;
     }
   }
 
   @SuppressWarnings("unchecked")
-  private TypeDetails evaluateFunctionType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
+  private TypeDetails evaluateFunctionType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, Set<ElementDefinition> elementDependencies,  ExpressionNode container) throws PathEngineException, DefinitionException {
     List<TypeDetails> paramTypes = new ArrayList<TypeDetails>();
     if (exp.getFunction() == Function.Is || exp.getFunction() == Function.As || exp.getFunction() == Function.OfType) {
       paramTypes.add(new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
@@ -3164,6 +3180,12 @@ public class FHIRPathEngine {
     } else {
       evaluateParameters(context, focus, exp, elementDependencies, paramTypes, false);
     }
+    if (exp.getFunction() == Function.First || exp.getFunction() == Function.Last || exp.getFunction() == Function.Tail || exp.getFunction() == Function.Skip || exp.getFunction() == Function.Take) {
+      if (focus.getCollectionStatus() == CollectionStatus.SINGLETON) {
+        typeWarnings.add(worker.formatMessage(I18nConstants.FHIRPATH_NOT_A_COLLECTION, container.toString()));
+
+      }
+    }
     switch (exp.getFunction()) {
     case Empty : 
       return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
@@ -5926,6 +5948,9 @@ public class FHIRPathEngine {
 
           ElementDefinitionMatch ed = getElementDefinition(sdi, path, isAllowPolymorphicNames(), expr);
           if (ed != null) {
+            if (ed.getDefinition().isChoice()) {
+              result.setChoice(true);
+            }
             if (!Utilities.noString(ed.getFixedType())) {
               if (elementDependencies != null) {
                 elementDependencies.add(ed.definition);
@@ -6024,7 +6049,11 @@ public class FHIRPathEngine {
       if (ed.getPath().equals(path)) {
         if (ed.hasContentReference()) {
           ElementDefinitionMatch res = getElementDefinitionById(sd, ed.getContentReference());
+          if (res == null) {
+            throw new Error("Unable to find "+ed.getContentReference());
+          } else {
             res.sourceDefinition = ed;
+          }
           return res;
         } else {
           return new ElementDefinitionMatch(ed, null);
@@ -6055,7 +6084,11 @@ public class FHIRPathEngine {
       if (ed.hasContentReference() && path.startsWith(ed.getPath()+".")) {
         ElementDefinitionMatch m = getElementDefinitionById(sd, ed.getContentReference());
         ElementDefinitionMatch res = getElementDefinition(sd, m.definition.getPath()+path.substring(ed.getPath().length()), allowTypedName, expr);
+        if (res == null) {
+          throw new Error("Unable to find "+ed.getContentReference());
+        } else {
           res.sourceDefinition = ed;
+        }
         return res;
       }
     }
@@ -6090,6 +6123,9 @@ public class FHIRPathEngine {
   }
 
   private ElementDefinitionMatch getElementDefinitionById(StructureDefinition sd, String ref) {
+    if (ref.startsWith(sd.getUrl()+"#")) {
+      ref = ref.replace(sd.getUrl()+"#", "#"); 
+    }
     for (ElementDefinition ed : sd.getSnapshot().getElement()) {
       if (ref.equals("#"+ed.getId())) {
         return new ElementDefinitionMatch(ed, null);
@@ -6411,4 +6447,13 @@ public class FHIRPathEngine {
   public void setAllowDoubleQuotes(boolean allowDoubleQuotes) {
     this.allowDoubleQuotes = allowDoubleQuotes;    
   }
+
+  public boolean isEmitSQLonFHIRWarning() {
+    return emitSQLonFHIRWarning;
+  }
+
+  public void setEmitSQLonFHIRWarning(boolean emitSQLonFHIRWarning) {
+    this.emitSQLonFHIRWarning = emitSQLonFHIRWarning;
+  }
+  
 }

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

@@ -73,7 +73,7 @@ import org.hl7.fhir.utilities.npm.ToolsVersion;
 public class NPMPackageGenerator {
 
   public enum Category {
-    RESOURCE, EXAMPLE, OPENAPI, SCHEMATRON, RDF, OTHER, TOOL, TEMPLATE, JEKYLL;
+    RESOURCE, EXAMPLE, OPENAPI, SCHEMATRON, RDF, OTHER, TOOL, TEMPLATE, JEKYLL, TEST;
 
     private String getDirectory() {
       switch (this) {
@@ -85,6 +85,7 @@ public class NPMPackageGenerator {
       case OTHER: return "package/other/";      
       case TEMPLATE: return "package/other/";      
       case JEKYLL: return "package/jekyll/";      
+      case TEST: return "package/tests/"; 
       case TOOL: return "package/bin/";      
       }
       return "/";

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

@@ -74,6 +74,7 @@ import java.util.HashSet;
 import org.apache.commons.lang3.StringUtils;
 import org.fhir.ucum.Utilities;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.model.BackboneElement;
 import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.r5.model.BooleanType;
 import org.hl7.fhir.r5.model.CanonicalType;
@@ -205,7 +206,7 @@ public class ToolingExtensions {
   public static final String EXT_VS_KEYWORD = "http://hl7.org/fhir/StructureDefinition/valueset-keyWord";  
   public static final String EXT_WORKGROUP = "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg";
   public static final String EXT_XML_NAMESPACE = "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace";
-  public static final String EXT_OLD_CONCEPTMAP_EQUIVALENCE = "http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.element.target.equivalence";
+  public static final String EXT_OLD_CONCEPTMAP_EQUIVALENCE = "http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.group.element.target.equivalence";
   public static final String EXT_Q_IS_SUBJ = "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-isSubject"; 
   public static final String EXT_Q_HIDDEN = "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden";
   public static final String EXT_Q_OTP_DISP = "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-optionalDisplay"; 
@@ -674,6 +675,28 @@ public class ToolingExtensions {
       resource.getExtension().add(new Extension(uri).setValue(new CodeType(value)));
   }
 
+  public static void setCodeExtensionMod(DomainResource resource, String uri, String value) {
+    if (Utilities.noString(value))
+      return;
+
+    Extension ext = getExtension(resource, uri);
+    if (ext != null)
+      ext.setValue(new CodeType(value));
+    else
+      resource.getModifierExtension().add(new Extension(uri).setValue(new CodeType(value)));
+  }
+
+  public static void setCodeExtensionMod(BackboneElement resource, String uri, String value) {
+    if (Utilities.noString(value))
+      return;
+
+    Extension ext = getExtension(resource, uri);
+    if (ext != null)
+      ext.setValue(new CodeType(value));
+    else
+      resource.getModifierExtension().add(new Extension(uri).setValue(new CodeType(value)));
+  }
+
   public static void setCodeExtension(Element element, String uri, String value) {
     if (Utilities.noString(value))
       return;

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/sql/Runner.java

@@ -74,6 +74,7 @@ public class Runner implements IEvaluationContext {
     }
     fpe = new FHIRPathEngine(context);
     fpe.setHostServices(this);
+    fpe.setEmitSQLonFHIRWarning(true);
     if (viewDefinition == null) {
       throw new FHIRException("No viewDefinition provided");
     }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/structuremap/StructureMapUtilities.java

@@ -1256,7 +1256,7 @@ public class StructureMapUtilities {
       vars.add(VariableMode.OUTPUT, getInputName(g, StructureMapInputMode.TARGET, "target"), target);
     else if (getInputName(g, StructureMapInputMode.TARGET, null) != null) {
       String type = getInputType(g, StructureMapInputMode.TARGET);
-      throw new Error("not handled yet: creating a type of " + type);
+      throw new FHIRException("not handled yet: creating a type of " + type);
     }
 
     executeGroup("", context, map, vars, g, true);
@@ -1424,7 +1424,7 @@ public class StructureMapUtilities {
     Set<String> check = new HashSet<String>();
     for (StructureMap sm : res) {
       if (check.contains(sm.getUrl()))
-        throw new Error("duplicate");
+        throw new FHIRException("duplicate");
       else
         check.add(sm.getUrl());
     }
@@ -1753,7 +1753,7 @@ public class StructureMapUtilities {
             else if (srcVar != null) {
               tn = determineTypeFromSourceType(map, group, vars.get(VariableMode.INPUT, srcVar), types);
             } else
-              throw new Error("Cannot determine type implicitly because there is no single input variable");
+              throw new FHIRException("Cannot determine type implicitly because there is no single input variable");
           } else {
             tn = getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString());
             // ok, now we resolve the type name against the import statements
@@ -1799,7 +1799,7 @@ public class StructureMapUtilities {
           }
           return new StringType(src);
         case ESCAPE:
-          throw new Error("Rule \"" + rulePath + "\": Transform " + tgt.getTransform().toCode() + " not supported yet");
+          throw new FHIRException("Rule \"" + rulePath + "\": Transform " + tgt.getTransform().toCode() + " not supported yet");
         case CAST:
           src = getParamString(vars, tgt.getParameter().get(0));
           if (tgt.getParameter().size() == 1)
@@ -1870,7 +1870,7 @@ public class StructureMapUtilities {
             return new StringType(b.fhirType() + "/" + id);
           }
         case DATEOP:
-          throw new Error("Rule \"" + rulePath + "\": Transform " + tgt.getTransform().toCode() + " not supported yet");
+          throw new FHIRException("Rule \"" + rulePath + "\": Transform " + tgt.getTransform().toCode() + " not supported yet");
         case UUID:
           return new IdType(UUID.randomUUID().toString());
         case POINTER:
@@ -1887,7 +1887,7 @@ public class StructureMapUtilities {
           Coding c = buildCoding(getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString()), getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString()));
           return c;
         default:
-          throw new Error("Rule \"" + rulePath + "\": Transform Unknown: " + tgt.getTransform().toCode());
+          throw new FHIRException("Rule \"" + rulePath + "\": Transform Unknown: " + tgt.getTransform().toCode());
       }
     } catch (Exception e) {
       throw new FHIRException("Exception executing transform " + tgt.toString() + " on Rule \"" + rulePath + "\": " + e.getMessage(), e);
@@ -2214,7 +2214,7 @@ public class StructureMapUtilities {
       TypeDetails type = new TypeDetails(CollectionStatus.SINGLETON);
       for (TypeRefComponent tr : element.getDefinition().getType()) {
         if (!tr.hasCode())
-          throw new Error("Rule \"" + ruleId + "\": Element has no type");
+          throw new FHIRException("Rule \"" + ruleId + "\": Element has no type");
         ProfiledType pt = new ProfiledType(tr.getWorkingCode());
         if (tr.hasProfile())
           pt.addProfiles(tr.getProfile());
@@ -2268,7 +2268,7 @@ public class StructureMapUtilities {
       }
       if (mapsSrc) {
         if (var == null)
-          throw new Error("Rule \"" + ruleId + "\": Attempt to assign with no context");
+          throw new FHIRException("Rule \"" + ruleId + "\": Attempt to assign with no context");
         tw.valueAssignment(tgt.getContext(), var.getProperty().getPath() + "." + tgt.getElement() + getTransformSuffix(tgt.getTransform()));
       } else if (tgt.hasContext()) {
         if (isSignificantElement(var.getProperty(), tgt.getElement())) {
@@ -2531,8 +2531,10 @@ public class StructureMapUtilities {
         TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON);
         td.addType("Reference", profile);
         return td;
+      case UUID:
+        return new TypeDetails(CollectionStatus.SINGLETON, "id");
       default:
-        throw new Error("Transform Unknown or not handled yet: " + tgt.getTransform().toCode());
+        throw new FHIRException("Transform Unknown or not handled yet: " + tgt.getTransform().toCode());
     }
   }
 

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

@@ -1003,6 +1003,9 @@ public class I18nConstants {
   public static final String CONCEPTMAP_VS_CONCEPT_CODE_UNKNOWN_SYSTEM = "CONCEPTMAP_VS_CONCEPT_CODE_UNKNOWN_SYSTEM";
   public static final String LOGICAL_MODEL_NAME_MISMATCH = "LOGICAL_MODEL_NAME_MISMATCH";
   public static final String LOGICAL_MODEL_QNAME_MISMATCH = "LOGICAL_MODEL_QNAME_MISMATCH";
+  public static final String FHIRPATH_CHOICE_NO_TYPE_SPECIFIER = "FHIRPATH_CHOICE_NO_TYPE_SPECIFIER";
+  public static final String FHIRPATH_CHOICE_SPURIOUS_TYPE_SPECIFIER = "FHIRPATH_CHOICE_SPURIOUS_TYPE_SPECIFIER";
+  public static final String FHIRPATH_NOT_A_COLLECTION = "FHIRPATH_NOT_A_COLLECTION";
 }
 
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/validation/IDigitalSignatureServices.java

@@ -0,0 +1,11 @@
+package org.hl7.fhir.utilities.validation;
+
+import java.io.IOException;
+
+import org.hl7.fhir.utilities.json.JsonException;
+import org.hl7.fhir.utilities.json.model.JsonObject;
+
+public interface IDigitalSignatureServices {
+
+  JsonObject fetchJWKS(String address) throws JsonException, IOException;
+}

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

@@ -736,8 +736,8 @@ BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_MODE = This is not a matching resource t
 BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_OUTCOME = This is not an OperationOutcome ({0})
 BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_NO_MODE = This is not a matching resource type for the specified search (is a search mode needed?) ({0} expecting {1})
 BUNDLE_SEARCH_NO_MODE = SearchSet bundles should have search modes on the entries
-INV_FAILED = Rule {0} Failed
+INV_FAILED = Constraint failed: {0} 
-INV_FAILED_SOURCE = Rule {0} Failed (defined in {1})
+INV_FAILED_SOURCE = Constraint failed: {0} (defined in {1})
 PATTERN_CHECK_STRING = The pattern [{0}] defined in the profile {1} not found. Issues: {2}
 TYPE_SPECIFIC_CHECKS_DT_URL_EXAMPLE = Example URLs are not allowed in this context ({0})
 UNICODE_BIDI_CONTROLS_CHARS_DISALLOWED = The Unicode sequence has bi-di control characters which are not allowed in this context: {0}
@@ -1060,3 +1060,7 @@ TYPE_SPECIFIC_CHECKS_DT_QTY_UCUM_ANNOTATIONS_NOT_IN_UNIT = UCUM Codes that conta
 TYPE_SPECIFIC_CHECKS_DT_QTY_UCUM_ANNOTATIONS = UCUM Codes that contain human readable annotations like {0} can be misleading (e.g. they are ignored when comparing units). Best Practice is not to depend on annotations in the UCUM code, so this usage should be checked
 LOGICAL_MODEL_NAME_MISMATCH = The name ''{0}'' does not match the expected name ''{1}''
 LOGICAL_MODEL_QNAME_MISMATCH = The QName ''{0}'' does not match the expected QName ''{1}''
+FHIRPATH_CHOICE_NO_TYPE_SPECIFIER = The expression ''{0}'' refers to an element that is a choice, but doesn''t have an .ofType() so that SQL view runners can pre-determine the full element name
+FHIRPATH_CHOICE_SPURIOUS_TYPE_SPECIFIER = The expression ''{0}'' refers to an element that is not a choice, but has an .ofType(). SQL view runners are likely to pre-determine an incorrect full element name
+FHIRPATH_NOT_A_COLLECTION = Found a use of a collection operator on something that is not a collection at ''{0}'' - check that there's no mistakes in the expression syntax
+

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java

@@ -185,6 +185,7 @@ import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
 import org.hl7.fhir.utilities.json.model.JsonObject;
+import org.hl7.fhir.utilities.validation.IDigitalSignatureServices;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
@@ -493,6 +494,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   public List<ValidatedFragment> validatedContent;
   public boolean testMode;
   private boolean example ;
+  private IDigitalSignatureServices signatureServices;
 
   public InstanceValidator(@Nonnull IWorkerContext theContext, @Nonnull IEvaluationContext hostServices, @Nonnull XVerExtensionManager xverManager) {
     super(theContext, xverManager, false);
@@ -710,6 +712,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     if (parser instanceof JsonParser) {
       ((JsonParser) parser).setAllowComments(allowComments);
     }
+    parser.setSignatureServices(signatureServices);
+    
     long t = System.nanoTime();
     validatedContent = null;
     try {
@@ -5586,9 +5590,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             long t = System.nanoTime();
             StructureDefinition profile = this.context.fetchResource(StructureDefinition.class, typeForResource.getProfile().get(0).asStringValue(), parentProfile);
             timeTracker.sd(t);
-            trackUsage(profile, valContext, element);
             if (rule(errors, NO_RULE_DATE, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(),
-                profile != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOPROFILE_EXPL, special.toHuman(), resourceName, typeForResource.getProfile().get(0).asStringValue())) {
+                profile != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOPROFILE_EXPL, special == null ? "??" : special.toHuman(), resourceName, typeForResource.getProfile().get(0).asStringValue())) {
+              trackUsage(profile, valContext, element);
               ok = validateResource(hc, errors, resource, element, profile, idstatus, stack, pct, mode) && ok;
             } else {
               ok = false;
@@ -5841,6 +5845,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     boolean ok = true;
     List<String> profiles = new ArrayList<String>();
     String type = null;
+    String typeName = null;
     ElementDefinition typeDefn = null;
     checkMustSupport(profile, ei);
     long s = System.currentTimeMillis();
@@ -5848,21 +5853,29 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     if (checkDefn.getType().size() == 1 && !"*".equals(checkDefn.getType().get(0).getWorkingCode()) && !"Element".equals(checkDefn.getType().get(0).getWorkingCode())
       && !"BackboneElement".equals(checkDefn.getType().get(0).getWorkingCode())) {
       type = checkDefn.getType().get(0).getWorkingCode();
+      typeName = type;
+      if (Utilities.isAbsoluteUrl(type)) {
+        StructureDefinition sdt = context.fetchTypeDefinition(type);
+        if (sdt != null) {
+          typeName = sdt.getTypeName();
+        }
+      }
       String stype = ei.getElement().fhirType();
       if (!stype.equals(type)) {
         if (checkDefn.isChoice()) {
           if (extensionUrl != null && !isAbsolute(extensionUrl)) {
             ok = rule(errors, NO_RULE_DATE, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), false, I18nConstants.EXTENSION_PROF_TYPE, profile.getVersionedUrl(), type, stype) && ok;
           } else if (!isAbstractType(type) && !"Extension".equals(profile.getType())) {
-            ok = rule(errors, NO_RULE_DATE, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), stype.equals(type), I18nConstants.EXTENSION_PROF_TYPE, profile.getVersionedUrl(), type, stype) && ok;                  
+            ok = rule(errors, NO_RULE_DATE, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), stype.equals(typeName), I18nConstants.EXTENSION_PROF_TYPE, profile.getVersionedUrl(), type, stype) && ok;                  
          }
         } else if (!isAbstractType(type)) {
-          ok = rule(errors, NO_RULE_DATE, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), stype.equals(type) || 
+          ok = rule(errors, NO_RULE_DATE, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), stype.equals(typeName) || 
             (Utilities.existsInList(type, "string", "id") && Utilities.existsInList(stype, "string", "id")), // work around a r4 problem with id/string
             I18nConstants.EXTENSION_PROF_TYPE, profile.getVersionedUrl(), type, stype) && ok;
         } else if (!isResource(type)) {
 //          System.out.println("update type "+type+" to "+stype+"?");
           type = stype;
+          typeName = type;
         } else {
           // this will be sorted out in contains ... System.out.println("update type "+type+" to "+stype+"?");
         }
@@ -5878,8 +5891,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       String prefix = tail(checkDefn.getPath());
       assert prefix.endsWith("[x]");
       type = ei.getName().substring(prefix.length() - 3);
-      if (isPrimitiveType(type))
+      typeName = type;
+      if (isPrimitiveType(type)) {
         type = Utilities.uncapitalize(type);
+        typeName = type;
+      }
       if (checkDefn.getType().get(0).hasProfile()) {
         for (CanonicalType p : checkDefn.getType().get(0).getProfile()) {
           profiles.add(p.getValue());
@@ -5892,13 +5908,16 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
 
       if (checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR)) {
         type = ei.getElement().getType();
+        typeName = type;
       } else if (ei.getElement().isResource()) {
         type = ei.getElement().fhirType();
+        typeName = type;            
       } else {
         prefix = prefix.substring(0, prefix.length() - 3);
         for (TypeRefComponent t : checkDefn.getType())
           if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) {
             type = t.getWorkingCode();
+            typeName = type;
             // Excluding reference is a kludge to get around versioning issues
             if (t.hasProfile() && !type.equals("Reference"))
               profiles.add(t.getProfile().get(0).getValue());
@@ -5906,9 +5925,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       }
       if (type == null) {
         TypeRefComponent trc = checkDefn.getType().get(0);
-        if (trc.getWorkingCode().equals("Reference"))
+        if (trc.getWorkingCode().equals("Reference")) {
           type = "Reference";
-        else
+          typeName = type;
+        } else
           ok = rule(errors, NO_RULE_DATE, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOTYPE, ei.getName(), describeTypes(checkDefn.getType())) && ok;
       }
     } else if (checkDefn.getContentReference() != null) {
@@ -5933,6 +5953,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
           ei.definition = ei.definition;            
         }
         type = null;
+        typeName = type;
       }
     }
     NodeStack localStack = stack.push(ei.getElement(), "*".equals(ei.getDefinition().getBase().getMax()) && ei.count == -1 ? 0 : ei.count, checkDefn, type == null ? typeDefn : resolveType(type, checkDefn.getType()));
@@ -7115,4 +7136,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     this.example = example;
     return this;
   }
+
+  public IDigitalSignatureServices getSignatureServices() {
+    return signatureServices;
+  }
+
+  public void setSignatureServices(IDigitalSignatureServices signatureServices) {
+    this.signatureServices = signatureServices;
+  }
+  
 }

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java

@@ -70,11 +70,13 @@ import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
+import org.hl7.fhir.utilities.json.JsonException;
 import org.hl7.fhir.utilities.json.JsonTrackingParser;
 import org.hl7.fhir.utilities.json.JsonUtilities;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.settings.FhirSettings;
 import org.hl7.fhir.utilities.tests.CacheVerificationLogger;
+import org.hl7.fhir.utilities.validation.IDigitalSignatureServices;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.validation.IgLoader;
 import org.hl7.fhir.validation.ValidationEngine;
@@ -98,7 +100,7 @@ import com.google.gson.JsonObject;
 
 
 @RunWith(Parameterized.class)
-public class ValidationTests implements IEvaluationContext, IValidatorResourceFetcher, IValidationPolicyAdvisor {
+public class ValidationTests implements IEvaluationContext, IValidatorResourceFetcher, IValidationPolicyAdvisor, IDigitalSignatureServices {
 
   public class TestSorter implements Comparator<Object> {
 
@@ -319,6 +321,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
     if (content.has("noHtmlInMarkdown")) {
       val.setHtmlInMarkdownCheck(HtmlInMarkdownCheck.ERROR);
     }
+    val.setSignatureServices(this);
     if (content.has("logical")==false) {
       val.setAssumeValidRestReferences(content.has("assumeValidRestReferences") ? content.get("assumeValidRestReferences").getAsBoolean() : false);
       logOutput(String.format("Start Validating (%d to set up)", (System.nanoTime() - setup) / 1000000));
@@ -792,4 +795,13 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
     return false;
   }
 
+  @Override
+  public org.hl7.fhir.utilities.json.model.JsonObject fetchJWKS(String address) throws JsonException, IOException {
+    if ("https://test.fhir.org/icao/.well-known/jwks.json".equals(address)) {
+      return org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(TestingUtilities.loadTestResourceBytes("validator", "test.fhir.org-jwks.json"));
+    } else {
+      return org.hl7.fhir.utilities.json.parser.JsonParser.parseObjectFromUrl(address);
+    }
+  }
+
 }

pom.xml

@@ -20,7 +20,7 @@
     <properties>
         <guava_version>32.0.1-jre</guava_version>
         <hapi_fhir_version>6.4.1</hapi_fhir_version>
-        <validator_test_case_version>1.4.8</validator_test_case_version>
+        <validator_test_case_version>1.4.9-SNAPSHOT</validator_test_case_version>
         <jackson_version>2.15.2</jackson_version>
         <junit_jupiter_version>5.9.2</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>