Merge remote-tracking branch 'origin/master' into do-20240830-maven-compiler-update

RELEASE_NOTES.md

@@ -1,7 +1,18 @@
 ## Validator Changes
 
-* no changes
+* Fix expression for con-3 properly (fix validation problem on some condition resources)
+* Fix FHIRPath bug using wrong type on simple elements when checking FHIRPath types
+* FHIRPath: Allow _ in constant names (per FHIRPath spec)
+* Fix value set rendering creating wrong references
+* Fix bug processing value set includes / excludes that are just value sets (no system value)
+* Alter processing of unknown code systems per discussion at ,https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/Don't.20error.20when.20you.20can't.20find.20code.20system and implement unknown-codesystems-cause-errors
+* Improve message for when elements are out of order in profile differentials
+
 
 ## Other code changes
 
-* no changes
+* fix problem where profile rendering had spurious 'slices for' nodes everywhere
+* Update SQL-On-FHIR implementation for latest cases, and clone test cases to general test care repository
+* Fix problem generating value set spreadsheets
+* fix concurrent modification error processing language translations
+* Check for null fetcher processing ConceptMaps (#1728)

org.hl7.fhir.convertors/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.3.24-SNAPSHOT</version>
+        <version>6.3.26-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.3.24-SNAPSHOT</version>
+		<version>6.3.26-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu2016may/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.3.24-SNAPSHOT</version>
+		<version>6.3.26-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu3/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.3.24-SNAPSHOT</version>
+        <version>6.3.26-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.3.24-SNAPSHOT</version>
+		<version>6.3.26-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r4b/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.3.24-SNAPSHOT</version>
+		<version>6.3.26-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.3.24-SNAPSHOT</version>
+		<version>6.3.26-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfilePathProcessor.java

@@ -289,7 +289,7 @@ public class ProfilePathProcessor {
       start++;
     } else {
       // we're just going to accept the differential slicing at face value
-      ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy());
+      ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy(), true);
       outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
       profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
 
@@ -667,14 +667,14 @@ public class ProfilePathProcessor {
       // some of what's in currentBase overrides template
       template = profileUtilities.fillOutFromBase(template, currentBase);
 
-    ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), template);
+    ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), template, true);
     outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
 
     res = outcome;
     profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
     if (diffMatches.get(0).hasSliceName()) {
       template = currentBase.copy();
-      template = profileUtilities.updateURLs(getUrl(), getWebUrl(), template);
+      template = profileUtilities.updateURLs(getUrl(), getWebUrl(), template, true);
       template.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), template.getPath(), getRedirector(), getContextPathSource()));
 
       checkToSeeIfSlicingExists(diffMatches.get(0), template);
@@ -866,13 +866,13 @@ public class ProfilePathProcessor {
 
 
   private void processSimplePathWithEmptyDiffMatches(ElementDefinition currentBase, String currentBasePath, List<ElementDefinition> diffMatches, ProfilePathProcessorState cursors, MappingAssistant mapHelper) {
-    ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy());
+    ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy(), true);
     outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
     profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
     profileUtilities.updateConstraintSources(outcome, getSourceStructureDefinition().getUrl());
     profileUtilities.checkExtensions(outcome);
     profileUtilities.updateFromObligationProfiles(outcome);
-    profileUtilities.updateURLs(url, webUrl, outcome);
+    profileUtilities.updateURLs(url, webUrl, outcome, true);
     profileUtilities.markDerived(outcome);
     if (cursors.resultPathBase == null)
       cursors.resultPathBase = outcome.getPath();
@@ -1033,7 +1033,7 @@ public class ProfilePathProcessor {
       if (!currentBase.isChoice() && !profileUtilities.ruleMatches(dSlice.getRules(), bSlice.getRules()))
         throw new DefinitionException(profileUtilities.getContext().formatMessage(I18nConstants.SLICING_RULES_ON_DIFFERENTIAL__DO_NOT_MATCH_THOSE_ON_BASE___RULE___, profileUtilities.summarizeSlicing(dSlice), profileUtilities.summarizeSlicing(bSlice), path, cursors.contextName));
     }
-    ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy());
+    ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy(), true);
     outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
     profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
     if (diffMatches.get(0).hasSlicing() || !diffMatches.get(0).hasSliceName()) {
@@ -1095,7 +1095,7 @@ public class ProfilePathProcessor {
       // We need to copy children of the backbone element before we start messing around with slices
       int newBaseLimit = profileUtilities.findEndOfElement(cursors.base, cursors.baseCursor);
       for (int i = cursors.baseCursor + 1; i <= newBaseLimit; i++) {
-        outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), cursors.base.getElement().get(i).copy());
+        outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), cursors.base.getElement().get(i).copy(), true);
         outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
         debugCheck(outcome);
         getResult().getElement().add(outcome);
@@ -1106,7 +1106,7 @@ public class ProfilePathProcessor {
     List<ElementDefinition> baseMatches = profileUtilities.getSiblings(cursors.base.getElement(), currentBase);
     for (ElementDefinition baseItem : baseMatches) {
       cursors.baseCursor = cursors.base.getElement().indexOf(baseItem);
-      outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), baseItem.copy());
+      outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), baseItem.copy(), true);
       profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
       outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
       outcome.setSlicing(null);
@@ -1139,7 +1139,7 @@ public class ProfilePathProcessor {
         cursors.baseCursor++;
         // just copy any children on the base
         while (cursors.baseCursor < cursors.base.getElement().size() && cursors.base.getElement().get(cursors.baseCursor).getPath().startsWith(path) && !cursors.base.getElement().get(cursors.baseCursor).getPath().equals(path)) {
-          outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), cursors.base.getElement().get(cursors.baseCursor).copy());
+          outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), cursors.base.getElement().get(cursors.baseCursor).copy(), true);
           outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
           if (!outcome.getPath().startsWith(cursors.resultPathBase))
             throw new DefinitionException(profileUtilities.getContext().formatMessage(I18nConstants.ADDING_WRONG_PATH));
@@ -1166,7 +1166,7 @@ public class ProfilePathProcessor {
         for (ElementDefinition baseItem : baseMatches)
           if (baseItem.getSliceName().equals(diffItem.getSliceName()))
             throw new DefinitionException(profileUtilities.getContext().formatMessage(I18nConstants.NAMED_ITEMS_ARE_OUT_OF_ORDER_IN_THE_SLICE));
-        outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy());
+        outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy(), true);
         //            outcome = updateURLs(url, diffItem.copy());
         outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
         profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
@@ -1409,7 +1409,7 @@ public class ProfilePathProcessor {
   private void processPathWithSlicedBaseAndEmptyDiffMatches(ElementDefinition currentBase, String currentBasePath, List<ElementDefinition> diffMatches, ProfilePathProcessorState cursors, String path, MappingAssistant mapHelper) {
     if (profileUtilities.hasInnerDiffMatches(getDifferential(), path, cursors.diffCursor, getDiffLimit(), cursors.base.getElement(), true)) {
       // so we just copy it in
-      ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy());
+      ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), currentBase.copy(), true);
       outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
       profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
       profileUtilities.markDerived(outcome);
@@ -1457,7 +1457,7 @@ public class ProfilePathProcessor {
       // the differential doesn't say anything about this item
       // copy across the currentbase, and all of its children and siblings
       while (cursors.baseCursor < cursors.base.getElement().size() && cursors.base.getElement().get(cursors.baseCursor).getPath().startsWith(path)) {
-        ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), cursors.base.getElement().get(cursors.baseCursor).copy());
+        ElementDefinition outcome = profileUtilities.updateURLs(getUrl(), getWebUrl(), cursors.base.getElement().get(cursors.baseCursor).copy(), true);
         outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
         if (!outcome.getPath().startsWith(cursors.resultPathBase))
           throw new DefinitionException(profileUtilities.getContext().formatMessage(I18nConstants.ADDING_WRONG_PATH_IN_PROFILE___VS_, getProfileName(), outcome.getPath(), cursors.resultPathBase));

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java

@@ -739,7 +739,7 @@ public class ProfileUtilities {
               if (existing != null) {
                 updateFromDefinition(existing, e, profileName, false, url, base, derived, "StructureDefinition.differential.element["+i+"]", mappingDetails);
               } else {
-                ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
+                ElementDefinition outcome = updateURLs(url, webUrl, e.copy(), true);
                 e.setUserData(UD_GENERATED_IN_SNAPSHOT, outcome);
                 derived.getSnapshot().addElement(outcome);
                 if (walksInto(diff.getElement(), e)) {
@@ -1042,7 +1042,7 @@ public class ProfileUtilities {
        // don't do this. should already be in snapshot ... addInheritedElementsForSpecialization(snapshot, focus, sd.getBaseDefinition(), path, url, weburl);
        for (ElementDefinition ed : sd.getSnapshot().getElement()) {
          if (ed.getPath().contains(".")) {
-           ElementDefinition outcome = updateURLs(url, weburl, ed.copy());
+           ElementDefinition outcome = updateURLs(url, weburl, ed.copy(), true);
            outcome.setPath(outcome.getPath().replace(sd.getTypeName(), path));
            snapshot.getElement().add(outcome);
          } else {
@@ -1548,7 +1548,6 @@ public class ProfileUtilities {
   protected void removeStatusExtensions(ElementDefinition outcome) {
     outcome.removeExtension(ToolingExtensions.EXT_FMM_LEVEL);
     outcome.removeExtension(ToolingExtensions.EXT_FMM_SUPPORT);
-    outcome.removeExtension(ToolingExtensions.EXT_FMM_DERIVED);
     outcome.removeExtension(ToolingExtensions.EXT_STANDARDS_STATUS);
     outcome.removeExtension(ToolingExtensions.EXT_NORMATIVE_VERSION);
     outcome.removeExtension(ToolingExtensions.EXT_WORKGROUP);    
@@ -1911,7 +1910,7 @@ public class ProfileUtilities {
    * @param element - the Element to update
    * @return - the updated Element
    */
-  public ElementDefinition updateURLs(String url, String webUrl, ElementDefinition element) {
+  public ElementDefinition updateURLs(String url, String webUrl, ElementDefinition element, boolean processRelatives) {
     if (element != null) {
       ElementDefinition defn = element;
       if (defn.hasBinding() && defn.getBinding().hasValueSet() && defn.getBinding().getValueSet().startsWith("#"))
@@ -1929,24 +1928,24 @@ public class ProfileUtilities {
       if (webUrl != null) {
         // also, must touch up the markdown
         if (element.hasDefinition()) {
-          element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
+          element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, processRelatives));
         }
         if (element.hasComment()) {
-          element.setComment(processRelativeUrls(element.getComment(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
+          element.setComment(processRelativeUrls(element.getComment(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, processRelatives));
         }
         if (element.hasRequirements()) {
-          element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
+          element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, processRelatives));
         }
         if (element.hasMeaningWhenMissing()) {
-          element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
+          element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, processRelatives));
         }
         if (element.hasBinding() && element.getBinding().hasDescription()) {
-          element.getBinding().setDescription(processRelativeUrls(element.getBinding().getDescription(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
+          element.getBinding().setDescription(processRelativeUrls(element.getBinding().getDescription(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, processRelatives));
         }
         for (Extension ext : element.getExtension()) {
           if (ext.hasValueMarkdownType()) {
             MarkdownType md = ext.getValueMarkdownType();
-            md.setValue(processRelativeUrls(md.getValue(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
+            md.setValue(processRelativeUrls(md.getValue(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, processRelatives));
           }
         }
       }
@@ -2371,7 +2370,6 @@ public class ProfileUtilities {
     if (elist.size() == 2) {
       dest.getExtension().remove(elist.get(1));
     }
-    
     updateExtensionsFromDefinition(dest, source);
 
     for (ElementDefinition ed : obligationProfileElements) {
@@ -2423,6 +2421,9 @@ public class ProfileUtilities {
       if (e.hasDefinition()) {
         base.setDefinition(processRelativeUrls(e.getDefinition(), webroot, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, true));
       }
+      if (e.getBinding().hasDescription()) {
+        base.getBinding().setDescription(processRelativeUrls(e.getBinding().getDescription(), webroot, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, true));
+      }
       base.setShort(e.getShort());
       if (e.hasCommentElement())
         base.setCommentElement(e.getCommentElement());
@@ -2466,9 +2467,9 @@ public class ProfileUtilities {
       if (derived.hasDefinitionElement()) {
         if (derived.getDefinition().startsWith("..."))
           base.setDefinition(Utilities.appendDerivedTextToBase(base.getDefinition(), derived.getDefinition()));
-        else if (!Base.compareDeep(derived.getDefinitionElement(), base.getDefinitionElement(), false))
+        else if (!Base.compareDeep(derived.getDefinitionElement(), base.getDefinitionElement(), false)) {
           base.setDefinitionElement(derived.getDefinitionElement().copy());
-        else if (trimDifferential)
+        } else if (trimDifferential)
           derived.setDefinitionElement(null);
         else if (derived.hasDefinitionElement())
           derived.getDefinitionElement().setUserData(UD_DERIVATION_EQUALS, true);

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

@@ -934,10 +934,14 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
       throw new Error(formatMessage(I18nConstants.NO_VALUE_SET_IN_URL));
     }
     for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
-      codeSystemsUsed.add(inc.getSystem());
+      if (inc.hasSystem()) {
+        codeSystemsUsed.add(inc.getSystem());
+      }
     }
     for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
-      codeSystemsUsed.add(inc.getSystem());
+      if (inc.hasSystem()) {
+        codeSystemsUsed.add(inc.getSystem());
+      }
     }
 
     CacheToken cacheToken = txCache.generateExpandToken(vs, hierarchical);

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

@@ -366,7 +366,11 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
   public StructureDefinition fetchByJsonName(String key) {
     for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
       ElementDefinition ed = sd.getSnapshot().getElementFirstRep();
-      if (sd.getKind() == StructureDefinitionKind.LOGICAL && ed != null && ed.hasExtension(ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED) && 
+      if (/*sd.getKind() == StructureDefinitionKind.LOGICAL && */ 
+          // this is turned off because it's valid to use a FHIR type directly in
+          // an extension of this kind, and that can't be a logical model. Any profile on
+          // a type is acceptable as long as it has the json name on it  
+          ed != null && ed.hasExtension(ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED) && 
           key.equals(ToolingExtensions.readStringExtension(ed, ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED))) {
         return sd;
       }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/fhirpath/FHIRLexer.java

@@ -187,7 +187,7 @@ public class FHIRLexer {
           cursor++;
         } else
         while (cursor < source.length() && ((source.charAt(cursor) >= 'A' && source.charAt(cursor) <= 'Z') || (source.charAt(cursor) >= 'a' && source.charAt(cursor) <= 'z') || 
-            (source.charAt(cursor) >= '0' && source.charAt(cursor) <= '9') || source.charAt(cursor) == ':' || source.charAt(cursor) == '-'))
+            (source.charAt(cursor) >= '0' && source.charAt(cursor) <= '9') || source.charAt(cursor) == ':' || source.charAt(cursor) == '-' || source.charAt(cursor) == '_'))
           cursor++;
         current = source.substring(currentStart, cursor);
       } else if (ch == '/') {

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

@@ -773,6 +773,25 @@ public class FHIRPathEngine {
     return execute(new ExecutionContext(null, base != null && base.isResource() ? base : null, base != null && base.isResource() ? base : null, base, base), list, ExpressionNode, true);
   }
 
+
+  /**
+   * evaluate a path and return the matching elements
+   * 
+   * @param base - the object against which the path is being evaluated
+   * @param ExpressionNode - the parsed ExpressionNode statement to use
+   * @return
+   * @throws FHIRException 
+   * @
+   */
+  public List<Base> evaluate(Object appContext, Base base, ExpressionNode ExpressionNode) throws FHIRException {
+    List<Base> list = new ArrayList<Base>();
+    if (base != null) {
+      list.add(base);
+    }
+    log = new StringBuilder();
+    return execute(new ExecutionContext(appContext, base != null && base.isResource() ? base : null, base != null && base.isResource() ? base : null, base, base), list, ExpressionNode, true);
+  }
+  
   /**
    * evaluate a path and return the matching elements
    * 
@@ -3741,6 +3760,8 @@ public class FHIRPathEngine {
       }
       if ((focus.hasType("date") || focus.hasType("datetime") || focus.hasType("instant"))) {
         return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Decimal, TypeDetails.FP_DateTime);       
+      } else if ((focus.hasType("time"))) {
+          return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Time, TypeDetails.FP_Time);       
       } else if (focus.hasType("decimal") || focus.hasType("integer")) {
         return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Decimal);       
       } else {
@@ -6351,7 +6372,7 @@ public class FHIRPathEngine {
                   }
                   result.addTypes(worker.getResourceNames());
                 } else {
-                  pt = new ProfiledType(t.getCode());
+                  pt = new ProfiledType(t.getWorkingCode());
                 }
                 if (pt != null) {
                   if (t.hasProfile()) {

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

@@ -3431,7 +3431,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
       sdMapCache.put(url, sdCache); 
       String webroot = sd.getUserString("webroot"); 
       for (ElementDefinition e : sd.getSnapshot().getElement()) { 
-        context.getProfileUtilities().updateURLs(sd.getUrl(), webroot, e); 
+        context.getProfileUtilities().updateURLs(sd.getUrl(), webroot, e, false); 
         sdCache.put(e.getId(), e); 
       } 
     } 

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

@@ -754,16 +754,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
     if (ref == null) {
       ref = (String) cs.getWebPath();
     }
-    if (ref == null && cs.hasUserData("webroot")) {
+    return ref == null ? null : ref.replace("\\", "/");
-      ref = (String) cs.getUserData("webroot");
-    }
-    if (ref == null) {
-      return "?ngen-14?.html";
-    }
-    if (!ref.contains(".html")) {
-      ref = ref + ".html";
-    }
-    return ref.replace("\\", "/");
   }
 
   private void scanForDesignations(ValueSetExpansionContainsComponent c, List<String> langs, Map<String, String> designations) {
@@ -922,14 +913,18 @@ public class ValueSetRenderer extends TerminologyRenderer {
         td.addText(code);
     } else {
       String href = context.fixReference(getCsRef(e));
-      if (href.contains("#"))
+      if (href == null) {
-        href = href + "-"+Utilities.nmtokenize(code);
+        td.code().tx(code);        
-      else
+      } else {
-        href = href + "#"+e.getId()+"-"+Utilities.nmtokenize(code);
+        if (href.contains("#"))
-      if (isAbstract)
+          href = href + "-"+Utilities.nmtokenize(code);
-        td.ah(context.prefixLocalHref(href)).setAttribute("title", context.formatPhrase(RenderingContext.VS_ABSTRACT_CODE_HINT)).i().addText(code);
+        else
-      else
+          href = href + "#"+e.getId()+"-"+Utilities.nmtokenize(code);
-        td.ah(context.prefixLocalHref(href)).addText(code);
+        if (isAbstract)
+          td.ah(context.prefixLocalHref(href)).setAttribute("title", context.formatPhrase(RenderingContext.VS_ABSTRACT_CODE_HINT)).i().addText(code);
+        else
+          td.ah(context.prefixLocalHref(href)).addText(code);
+      }
     }
   }
 
@@ -1247,11 +1242,15 @@ public class ValueSetRenderer extends TerminologyRenderer {
               wli.tx(f.getProperty()+" "+describe(f.getOp())+" ");
               if (e != null && codeExistsInValueSet(e, f.getValue())) {
                 String href = getContext().fixReference(getCsRef(e));
-                if (href.contains("#"))
+                if (href == null) {
-                  href = href + "-"+Utilities.nmtokenize(f.getValue());
+                  wli.code().tx(f.getValue());                  
-                else
+                } else {
-                  href = href + "#"+e.getId()+"-"+Utilities.nmtokenize(f.getValue());
+                  if (href.contains("#"))
-                wli.ah(context.prefixLocalHref(href)).addText(f.getValue());
+                    href = href + "-"+Utilities.nmtokenize(f.getValue());
+                  else
+                    href = href + "#"+e.getId()+"-"+Utilities.nmtokenize(f.getValue());
+                  wli.ah(context.prefixLocalHref(href)).addText(f.getValue());
+                }
               } else if (inc.hasSystem()) {
                 wli.addText(f.getValue());
                 ValidationResult vr = getContext().getWorker().validateCode(getContext().getTerminologyServiceOptions(), inc.getSystem(), inc.getVersion(), f.getValue(), null);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/RenderingContext.java

@@ -554,6 +554,9 @@ public class RenderingContext extends RenderingI18nContext {
   }
 
   public String fixReference(String ref) {
+    if (ref == null) {
+      return null;
+    }
     if (!Utilities.isAbsoluteUrl(ref)) {
       return (localPrefix == null ? "" : localPrefix)+ref;
     }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/expansion/ValueSetExpander.java

@@ -606,33 +606,35 @@ public class ValueSetExpander extends ValueSetProcessBase {
       excludeCodes(wc, importValueSetForExclude(wc, imp.getValue(), exp, expParams, false, vs).getExpansion());
     }
     
-    CodeSystem cs = context.fetchSupplementedCodeSystem(exc.getSystem());
+    if (exc.hasSystem()) {
-    if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem(), opContext.getOptions().getFhirVersion())) {
+      CodeSystem cs = context.fetchSupplementedCodeSystem(exc.getSystem());
-      ValueSetExpansionOutcome vse = context.expandVS(exc, false, false);
+      if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem(), opContext.getOptions().getFhirVersion())) {
-      ValueSet valueset = vse.getValueset();
+        ValueSetExpansionOutcome vse = context.expandVS(exc, false, false);
-      if (valueset == null)
+        ValueSet valueset = vse.getValueset();
-        throw failTSE("Error Expanding ValueSet: "+vse.getError());
+        if (valueset == null)
-      excludeCodes(wc, valueset.getExpansion());
+          throw failTSE("Error Expanding ValueSet: "+vse.getError());
-      return;
+        excludeCodes(wc, valueset.getExpansion());
-    }
+        return;
-
-    for (ConceptReferenceComponent c : exc.getConcept()) {
-      excludeCode(wc, exc.getSystem(), c.getCode());
-    }
-
-    if (exc.getFilter().size() > 0) {
-      if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
-        addFragmentWarning(exp, cs);
       }
-      List<WorkingContext> filters = new ArrayList<>();
+
-      for (int i = 1; i < exc.getFilter().size(); i++) {
+      for (ConceptReferenceComponent c : exc.getConcept()) {
-        WorkingContext wc1 = new WorkingContext();
+        excludeCode(wc, exc.getSystem(), c.getCode());
-        filters.add(wc1);
+      }
-        processFilter(exc, exp, expParams, null, cs, false, exc.getFilter().get(i), wc1, null, true);
+
+      if (exc.getFilter().size() > 0) {
+        if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
+          addFragmentWarning(exp, cs);
+        }
+        List<WorkingContext> filters = new ArrayList<>();
+        for (int i = 1; i < exc.getFilter().size(); i++) {
+          WorkingContext wc1 = new WorkingContext();
+          filters.add(wc1);
+          processFilter(exc, exp, expParams, null, cs, false, exc.getFilter().get(i), wc1, null, true);
+        }
+        ConceptSetFilterComponent fc = exc.getFilter().get(0);
+        WorkingContext wc1 = dwc;
+        processFilter(exc, exp, expParams, null, cs, false, fc, wc1, filters, true);
       }
-      ConceptSetFilterComponent fc = exc.getFilter().get(0);
-      WorkingContext wc1 = dwc;
-      processFilter(exc, exp, expParams, null, cs, false, fc, wc1, filters, true);
     }
   }
 
@@ -728,7 +730,6 @@ public class ValueSetExpander extends ValueSetProcessBase {
       expParams = makeDefaultExpansion();
     altCodeParams.seeParameters(expParams);
     altCodeParams.seeValueSet(source);
-    
     source.checkNoModifiers("ValueSet", "expanding");
     focus = source.copy();
     focus.setIdBase(null);

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

@@ -124,11 +124,9 @@ public class ValueSetValidator extends ValueSetProcessBase {
     }
     public String getMessage() {
       return message;
-    }
+    } 
-    
   }
 
-
   private ValueSet valueset;
   private Map<String, ValueSetValidator> inner = new HashMap<>();
   private ValidationOptions options;

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

@@ -103,7 +103,7 @@ public class Runner implements IEvaluationContext {
       for (JsonObject w : vd.getJsonObjects("where")) {
         String expr = w.asString("path");
         ExpressionNode node = fpe.parse(expr);
-        boolean pass = fpe.evaluateToBoolean(null, b, b, b, node);
+        boolean pass = fpe.evaluateToBoolean(vd, b, b, b, node);
         if (!pass) {
           ok = false;
           break;
@@ -114,7 +114,7 @@ public class Runner implements IEvaluationContext {
         rows.add(new ArrayList<Cell>());
 
         for (JsonObject select : vd.getJsonObjects("select")) {
-          executeSelect(select, b, rows);
+          executeSelect(vd, select, b, rows);
         }
         for (List<Cell> row : rows) {
           storage.addRow(store, row);
@@ -124,14 +124,14 @@ public class Runner implements IEvaluationContext {
     storage.finish(store);
   }
   
-  private void executeSelect(JsonObject select, Base b, List<List<Cell>> rows) {
+  private void executeSelect(JsonObject vd, JsonObject select, Base b, List<List<Cell>> rows) {
     List<Base> focus = new ArrayList<>();
     
     if (select.has("forEach")) {
-      focus.addAll(executeForEach(select, b));
+      focus.addAll(executeForEach(vd, select, b));
     } else if (select.has("forEachOrNull")) {
       
-      focus.addAll(executeForEachOrNull(select, b));  
+      focus.addAll(executeForEachOrNull(vd, select, b));  
       if (focus.isEmpty()) {
         List<Column> columns = (List<Column>) select.getUserData("columns");
         for (List<Cell> row : rows) {
@@ -159,20 +159,20 @@ public class Runner implements IEvaluationContext {
       List<List<Cell>> rowsToAdd = cloneRows(tempRows);  
 
       for (JsonObject column : select.getJsonObjects("column")) {
-        executeColumn(column, f, rowsToAdd);
+        executeColumn(vd, column, f, rowsToAdd);
       }
 
       for (JsonObject sub : select.getJsonObjects("select")) {
-        executeSelect(sub, f, rowsToAdd);
+        executeSelect(vd, sub, f, rowsToAdd);
       }
       
-      executeUnionAll(select.getJsonObjects("unionAll"), f, rowsToAdd);
+      executeUnionAll(vd, select.getJsonObjects("unionAll"), f, rowsToAdd);
       
       rows.addAll(rowsToAdd);
     }
   }
 
-  private void executeUnionAll(List<JsonObject> unionList,  Base b, List<List<Cell>> rows) {
+  private void executeUnionAll(JsonObject vd, List<JsonObject> unionList,  Base b, List<List<Cell>> rows) {
     if (unionList.isEmpty()) {
       return;
     }
@@ -183,7 +183,7 @@ public class Runner implements IEvaluationContext {
     for (JsonObject union : unionList) {
       List<List<Cell>> tempRows = new ArrayList<>();
       tempRows.addAll(sourceRows);      
-      executeSelect(union, b, tempRows);
+      executeSelect(vd, union, b, tempRows);
       rows.addAll(tempRows);
     }
   }
@@ -204,25 +204,25 @@ public class Runner implements IEvaluationContext {
     return list;
   }
 
-  private List<Base> executeForEach(JsonObject focus, Base b) {
+  private List<Base> executeForEach(JsonObject vd, JsonObject focus, Base b) {
     ExpressionNode n = (ExpressionNode) focus.getUserData("forEach");
     List<Base> result = new ArrayList<>();
-    result.addAll(fpe.evaluate(b, n));
+    result.addAll(fpe.evaluate(vd, b, n));
     return result;  
   }
 
-  private List<Base> executeForEachOrNull(JsonObject focus, Base b) {
+  private List<Base> executeForEachOrNull(JsonObject vd, JsonObject focus, Base b) {
     ExpressionNode n = (ExpressionNode) focus.getUserData("forEachOrNull");
     List<Base> result = new ArrayList<>();
-    result.addAll(fpe.evaluate(b, n));
+    result.addAll(fpe.evaluate(vd, b, n));
     return result;  
   }
 
-  private void executeColumn(JsonObject column, Base b, List<List<Cell>> rows) {
+  private void executeColumn(JsonObject vd, JsonObject column, Base b, List<List<Cell>> rows) {
     ExpressionNode n = (ExpressionNode) column.getUserData("path");
     List<Base> bl2 = new ArrayList<>();
     if (b != null) {
-      bl2.addAll(fpe.evaluate(b, n));
+      bl2.addAll(fpe.evaluate(vd, b, n));
     }
     Column col = (Column) column.getUserData("column");
     if (col == null) {
@@ -344,14 +344,43 @@ public class Runner implements IEvaluationContext {
   
   @Override
   public List<Base> resolveConstant(FHIRPathEngine engine, Object appContext, String name, boolean beforeContext, boolean explicitConstant) throws PathEngineException {
-    throw new Error("Not implemented yet: resolveConstant");
+    List<Base> list = new ArrayList<Base>();
+    if (explicitConstant) {
+      JsonObject vd = (JsonObject) appContext;
+      JsonObject constant = findConstant(vd, name);
+      if (constant != null) {
+        Base b = (Base) constant.getUserData("value");
+        if (b != null) {
+          list.add(b);
+        }
+      }
+    }
+    return list;    
   }
 
   @Override
   public TypeDetails resolveConstantType(FHIRPathEngine engine, Object appContext, String name, boolean explicitConstant) throws PathEngineException {
-    throw new Error("Not implemented yet: resolveConstantType");
+    if (explicitConstant) {
+      JsonObject vd = (JsonObject) appContext;
+      JsonObject constant = findConstant(vd, name.substring(1));
+      if (constant != null) {
+        Base b = (Base) constant.getUserData("value");
+        if (b != null) {
+          return new TypeDetails(CollectionStatus.SINGLETON, b.fhirType());
+        }
+      }
+    }
+    return null;
   }
 
+  private JsonObject findConstant(JsonObject vd, String name) {
+    for (JsonObject o : vd.getJsonObjects("constant")) {
+      if (name.equals(o.asString("name"))) {
+        return o;
+      }
+    }
+    return null;
+  }
   @Override
   public boolean log(String argument, List<Base> focus) {
     throw new Error("Not implemented yet: log");

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

@@ -2,6 +2,7 @@ package org.hl7.fhir.r5.utils.sql;
 
 import java.util.List;
 
+import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.utilities.json.model.JsonArray;
 import org.hl7.fhir.utilities.json.model.JsonBoolean;
@@ -33,16 +34,16 @@ public class StorageJson implements Storage {
     JsonObject row = new JsonObject();
     rows.add(row);
     for (Cell cell : cells) {
-      if (cell.getValues().size() == 0) {
+      if (cell.getColumn().isColl() || cell.getValues().size() > 1) {
-        row.add(cell.getColumn().getName(), new JsonNull());
-      } else if (cell.getValues().size() == 1) {
-        row.add(cell.getColumn().getName(), makeJsonNode(cell.getValues().get(0)));
-      } else {
         JsonArray arr = new JsonArray();
-        row.add(cell.getColumn().getName(), arr);
+        row.add(cell.getColumn().getName(), arr);   
         for (Value value : cell.getValues()) {
           arr.add(makeJsonNode(value));
-        }
+        } 
+      } else if (cell.getValues().size() == 0) {
+        row.add(cell.getColumn().getName(), new JsonNull());
+      } else {
+        row.add(cell.getColumn().getName(), makeJsonNode(cell.getValues().get(0)));
       }
     }
   }
@@ -87,7 +88,7 @@ public class StorageJson implements Storage {
 
   @Override
   public String getKeyForSourceResource(Base res) {
-    return res.getIdBase();
+    return res.fhirType()+"/"+res.getIdBase();
   }
 
   @Override

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

@@ -11,6 +11,27 @@ import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.fhirpath.ExpressionNode;
 import org.hl7.fhir.r5.fhirpath.FHIRPathEngine;
 import org.hl7.fhir.r5.fhirpath.TypeDetails;
+import org.hl7.fhir.r5.formats.JsonParser;
+import org.hl7.fhir.r5.model.Base64BinaryType;
+import org.hl7.fhir.r5.model.BooleanType;
+import org.hl7.fhir.r5.model.CanonicalType;
+import org.hl7.fhir.r5.model.CodeType;
+import org.hl7.fhir.r5.model.DateTimeType;
+import org.hl7.fhir.r5.model.DateType;
+import org.hl7.fhir.r5.model.DecimalType;
+import org.hl7.fhir.r5.model.IdType;
+import org.hl7.fhir.r5.model.InstantType;
+import org.hl7.fhir.r5.model.Integer64Type;
+import org.hl7.fhir.r5.model.IntegerType;
+import org.hl7.fhir.r5.model.OidType;
+import org.hl7.fhir.r5.model.PositiveIntType;
+import org.hl7.fhir.r5.model.PrimitiveType;
+import org.hl7.fhir.r5.model.StringType;
+import org.hl7.fhir.r5.model.TimeType;
+import org.hl7.fhir.r5.model.UnsignedIntType;
+import org.hl7.fhir.r5.model.UriType;
+import org.hl7.fhir.r5.model.UrlType;
+import org.hl7.fhir.r5.model.UuidType;
 import org.hl7.fhir.r5.fhirpath.ExpressionNode.CollectionStatus;
 import org.hl7.fhir.r5.fhirpath.FHIRPathEngine.IssueMessage;
 import org.hl7.fhir.utilities.Utilities;
@@ -99,7 +120,7 @@ public class Validator {
         i = 0;
         if (checkAllObjects(path, viewDefinition, "where")) {
           for (JsonObject where : viewDefinition.getJsonObjects("where")) {
-            checkWhere(path+".where["+i+"]", where);
+            checkWhere(viewDefinition, path+".where["+i+"]", where);
             i++;
           }
         }
@@ -108,7 +129,7 @@ public class Validator {
         i = 0;
         if (checkAllObjects(path, viewDefinition, "select")) {
           for (JsonObject select : viewDefinition.getJsonObjects("select")) {
-            columns.addAll(checkSelect(path+".select["+i+"]", select, t));
+            columns.addAll(checkSelect(viewDefinition, path+".select["+i+"]", select, t));
             i++;
           }
           if (i == 0) {
@@ -119,15 +140,15 @@ public class Validator {
     }
   }
 
-  private List<Column> checkSelect(String path, JsonObject select, TypeDetails t) {
+  private List<Column> checkSelect(JsonObject vd, String path, JsonObject select, TypeDetails t) {
     List<Column> columns = new ArrayList<>();
     select.setUserData("columns", columns);
     checkProperties(select, path, "column", "select", "forEach", "forEachOrNull", "unionAll");
 
     if (select.has("forEach")) {
-      t = checkForEach(path, select, select.get("forEach"), t);
+      t = checkForEach(vd, path, select, select.get("forEach"), t);
     } else if (select.has("forEachOrNull")) {
-      t = checkForEachOrNull(path, select, select.get("forEachOrNull"), t);
+      t = checkForEachOrNull(vd, path, select, select.get("forEachOrNull"), t);
     } 
 
     if (t != null) {
@@ -142,7 +163,7 @@ public class Validator {
             if (!(e instanceof JsonObject)) {
               error(path+".column["+i+"]", a, "column["+i+"] is a "+e.type().toName()+" not an object", IssueType.INVALID);
             } else { 
-              columns.add(checkColumn(path+".column["+i+"]", (JsonObject) e, t));
+              columns.add(checkColumn(vd, path+".column["+i+"]", (JsonObject) e, t));
             }
           }      
         }     
@@ -158,14 +179,14 @@ public class Validator {
             if (!(e instanceof JsonObject)) {
               error(path+".select["+i+"]", e, "select["+i+"] is not an object", IssueType.INVALID);
             } else { 
-              columns.addAll(checkSelect(path+".select["+i+"]", (JsonObject) e, t));
+              columns.addAll(checkSelect(vd, path+".select["+i+"]", (JsonObject) e, t));
             }
           }      
         }     
       }
 
       if (select.has("unionAll")) {
-        columns.addAll(checkUnion(path, select, select.get("unionAll"), t));
+        columns.addAll(checkUnion(vd, path, select, select.get("unionAll"), t));
       } 
       if (columns.isEmpty()) {
         error(path, select, "The select has no columns or selects", IssueType.REQUIRED);
@@ -191,7 +212,7 @@ public class Validator {
     }    
   }
 
-  private List<Column> checkUnion(String path, JsonObject focus, JsonElement expression,  TypeDetails t) {
+  private List<Column> checkUnion(JsonObject vd, String path, JsonObject focus, JsonElement expression,  TypeDetails t) {
     JsonElement a = focus.get("unionAll");
     if (!(a instanceof JsonArray)) {
       error(path+".unionAll", a, "union is not an array", IssueType.INVALID);
@@ -203,7 +224,7 @@ public class Validator {
         if (!(e instanceof JsonObject)) {
           error(path+".unionAll["+i+"]", e, "unionAll["+i+"] is not an object", IssueType.INVALID);
         } else { 
-          unionColumns.add(checkSelect(path+".unionAll["+i+"]", (JsonObject) e, t));
+          unionColumns.add(checkSelect(vd, path+".unionAll["+i+"]", (JsonObject) e, t));
         }
         i++;
       }  
@@ -242,7 +263,7 @@ public class Validator {
     }
   }
 
-  private Column checkColumn(String path, JsonObject column, TypeDetails t) {
+  private Column checkColumn(JsonObject vd, String path, JsonObject column, TypeDetails t) {
     checkProperties(column, path, "path", "name", "description", "collection", "type", "tag");
 
     if (!column.has("path")) {
@@ -260,7 +281,7 @@ public class Validator {
         try {
           node = fpe.parse(expr);
           column.setUserData("path", node);
-          td = fpe.checkOnTypes(null, resourceName, t, node, warnings);
+          td = fpe.checkOnTypes(vd, resourceName, t, node, warnings);
         } catch (Exception e) {
           error(path, expression, e.getMessage(), IssueType.INVALID);
         }
@@ -296,25 +317,31 @@ public class Validator {
           // ok, name is sorted!
           if (columnName != null) {
             column.setUserData("name", columnName);
-            boolean isColl = (td.getCollectionStatus() != CollectionStatus.SINGLETON);
+            boolean isColl = false;
             if (column.has("collection")) {
               JsonElement collectionJ = column.get("collection");
               if (!(collectionJ instanceof JsonBoolean)) {
                 error(path+".collection", collectionJ, "collection is not a boolean", IssueType.INVALID);
               } else {
                 boolean collection = collectionJ.asJsonBoolean().asBoolean();
-                if (!collection && isColl) {
+                if (collection) {
-                  isColl = false;
+                  isColl = true;
-                  warning(path, column, "collection is false, but the path statement(s) might return multiple values for the column '"+columnName+"' some inputs");
                 }
               }
             }
             if (isColl) {
+              if (td.getCollectionStatus() == CollectionStatus.SINGLETON) {
+                hint(path, column, "collection is true, but the path statement(s) can only return single values for the column '"+columnName+"'");
+              }
+            } else {
               if (arrays == null) {
                 warning(path, expression, "The column '"+columnName+"' appears to be a collection based on it's path. Collections are not supported in all execution contexts");
               } else if (!arrays) {
                 warning(path, expression, "The column '"+columnName+"' appears to be a collection based on it's path, but this is not allowed in the current execution context");
               }
+              if (td.getCollectionStatus() != CollectionStatus.SINGLETON) {
+                warning(path, column, "collection is not true, but the path statement(s) might return multiple values for the column '"+columnName+"' for some inputs");
+              }
             }
             Set<String> types = new HashSet<>();
             if (node.isNullSet()) {
@@ -330,7 +357,7 @@ public class Validator {
                 if (typeJ instanceof JsonString) {
                   String type = typeJ.asString();
                   if (!td.hasType(type)) {
-                    error(path+".type", typeJ, "The path expression does not return a value of the type '"+type, IssueType.VALUE);
+                    error(path+".type", typeJ, "The path expression does not return a value of the type '"+type+"' - found "+td.describe(), IssueType.VALUE);
                   } else {
                     types.clear();
                     types.add(simpleType(type));
@@ -377,6 +404,8 @@ public class Validator {
     case "integer": return ColumnKind.Integer;
     case "decimal": return ColumnKind.Decimal;
     case "string": return ColumnKind.String;
+    case "id": return ColumnKind.String;
+    case "code": return ColumnKind.String;
     case "base64Binary": return ColumnKind.Binary;
     case "time": return ColumnKind.Time;
     default: return ColumnKind.Complex;
@@ -384,7 +413,7 @@ public class Validator {
   }
 
   private boolean isSimpleType(String type) {
-    return Utilities.existsInList(type, "dateTime", "boolean", "integer", "decimal", "string", "base64Binary");
+    return Utilities.existsInList(type, "dateTime", "boolean", "integer", "decimal", "string", "base64Binary", "id", "code", "date", "time");
   }
 
   private String simpleType(String type) {
@@ -413,7 +442,7 @@ public class Validator {
     return type;
   }
 
-  private TypeDetails checkForEach(String path, JsonObject focus, JsonElement expression, TypeDetails t) {
+  private TypeDetails checkForEach(JsonObject vd, String path, JsonObject focus, JsonElement expression, TypeDetails t) {
     if (!(expression instanceof JsonString)) {
       error(path+".forEach", expression, "forEach is not a string", IssueType.INVALID);
       return null;
@@ -425,7 +454,7 @@ public class Validator {
       try {
         ExpressionNode n = fpe.parse(expr);
         focus.setUserData("forEach", n);
-        td = fpe.checkOnTypes(null, resourceName, t, n, warnings);
+        td = fpe.checkOnTypes(vd, resourceName, t, n, warnings);
       } catch (Exception e) {
         error(path, expression, e.getMessage(), IssueType.INVALID);
       }
@@ -438,7 +467,7 @@ public class Validator {
     }
   }
 
-  private TypeDetails checkForEachOrNull(String path, JsonObject focus, JsonElement expression, TypeDetails t) {
+  private TypeDetails checkForEachOrNull(JsonObject vd, String path, JsonObject focus, JsonElement expression, TypeDetails t) {
     if (!(expression instanceof JsonString)) {
       error(path+".forEachOrNull", expression, "forEachOrNull is not a string", IssueType.INVALID);
       return null;
@@ -450,7 +479,7 @@ public class Validator {
       try {
         ExpressionNode n = fpe.parse(expr);
         focus.setUserData("forEachOrNull", n);
-        td = fpe.checkOnTypes(null, resourceName, t, n, warnings);
+        td = fpe.checkOnTypes(vd, resourceName, t, n, warnings);
       } catch (Exception e) {
         error(path, expression, e.getMessage(), IssueType.INVALID);
       }
@@ -477,69 +506,79 @@ public class Validator {
       }
     }
     if (constant.has("valueBase64Binary")) {
-      checkIsString(path, constant, "valueBase64Binary");
+      checkIsString(path, constant, "valueBase64Binary", new Base64BinaryType());
     } else if (constant.has("valueBoolean")) {
-      checkIsBoolean(path, constant, "valueBoolean");
+      checkIsBoolean(path, constant, "valueBoolean", new BooleanType());
     } else if (constant.has("valueCanonical")) { 
-      checkIsString(path, constant, "valueCanonical");
+      checkIsString(path, constant, "valueCanonical", new CanonicalType());
     } else if (constant.has("valueCode")) {
-      checkIsString(path, constant, "valueCode");
+      checkIsString(path, constant, "valueCode", new CodeType());
     } else if (constant.has("valueDate")) {
-      checkIsString(path, constant, "valueDate");
+      checkIsString(path, constant, "valueDate", new DateType());
     } else if (constant.has("valueDateTime")) {
-      checkIsString(path, constant, "valueDateTime");
+      checkIsString(path, constant, "valueDateTime", new DateTimeType());
     } else if (constant.has("valueDecimal")) {
-      checkIsNumber(path, constant, "valueDecimal");
+      checkIsNumber(path, constant, "valueDecimal", new DecimalType());
     } else if (constant.has("valueId")) {
-      checkIsString(path, constant, "valueId");
+      checkIsString(path, constant, "valueId", new IdType());
     } else if (constant.has("valueInstant")) {
-      checkIsString(path, constant, "valueInstant");
+      checkIsString(path, constant, "valueInstant", new InstantType());
     } else if (constant.has("valueInteger")) {
-      checkIsNumber(path, constant, "valueInteger");
+      checkIsNumber(path, constant, "valueInteger", new IntegerType());
     } else if (constant.has("valueInteger64")) {
-      checkIsNumber(path, constant, "valueInteger64");
+      checkIsNumber(path, constant, "valueInteger64", new Integer64Type());
     } else if (constant.has("valueOid")) {
-      checkIsString(path, constant, "valueOid");
+      checkIsString(path, constant, "valueOid", new OidType());
     } else if (constant.has("valueString")) {
-      checkIsString(path, constant, "valueString");
+      checkIsString(path, constant, "valueString", new StringType());
     } else if (constant.has("valuePositiveInt")) {
-      checkIsNumber(path, constant, "valuePositiveInt");
+      checkIsNumber(path, constant, "valuePositiveInt", new PositiveIntType());
     } else if (constant.has("valueTime")) {
-      checkIsString(path, constant, "valueTime");
+      checkIsString(path, constant, "valueTime", new TimeType());
     } else if (constant.has("valueUnsignedInt")) {
-      checkIsNumber(path, constant, "valueUnsignedInt");
+      checkIsNumber(path, constant, "valueUnsignedInt", new UnsignedIntType());
     } else if (constant.has("valueUri")) {
-      checkIsString(path, constant, "valueUri");
+      checkIsString(path, constant, "valueUri", new UriType());
     } else if (constant.has("valueUrl")) {
-      checkIsString(path, constant, "valueUrl");
+      checkIsString(path, constant, "valueUrl", new UrlType());
     } else if (constant.has("valueUuid")) {
-      checkIsString(path, constant, "valueUuid");
+      checkIsString(path, constant, "valueUuid", new UuidType());
     } else {
       error(path, constant, "No value found", IssueType.REQUIRED);
     }
   }
 
-  private void checkIsString(String path, JsonObject constant, String name) {
+  private void checkIsString(String path, JsonObject constant, String name, PrimitiveType<?> value) {
     JsonElement j = constant.get(name);
     if (!(j instanceof JsonString)) {
       error(path+"."+name, j, name+" must be a string", IssueType.INVALID);
+    } else {
+      value.setValueAsString(j.asString());
+      constant.setUserData("value", value);
     }
   }
 
-  private void checkIsBoolean(String path, JsonObject constant, String name) {
+  private void checkIsBoolean(String path, JsonObject constant, String name, PrimitiveType<?> value) {
     JsonElement j = constant.get(name);
     if (!(j instanceof JsonBoolean)) {
       error(path+"."+name, j, name+" must be a boolean", IssueType.INVALID);
+    } else {
+      value.setValueAsString(j.asString());
+      constant.setUserData("value", value);
     }
   }
 
-  private void checkIsNumber(String path, JsonObject constant, String name) {
+  private void checkIsNumber(String path, JsonObject constant, String name, PrimitiveType<?> value) {
     JsonElement j = constant.get(name);
     if (!(j instanceof JsonNumber)) {
       error(path+"."+name, j, name+" must be a number", IssueType.INVALID);
+    } else {
+      value.setValueAsString(j.asString());
+      constant.setUserData("value", value);
     }
   }
-  private void checkWhere(String path, JsonObject where) {
+  
+  private void checkWhere(JsonObject vd, String path, JsonObject where) {
     checkProperties(where, path, "path", "description");
 
     String expr = where.asString("path");
@@ -553,7 +592,7 @@ public class Validator {
     try {
       ExpressionNode n = fpe.parse(expr);
       where.setUserData("path", n);
-      td = fpe.checkOnTypes(null, resourceName, types, n, warnings);
+      td = fpe.checkOnTypes(vd, resourceName, types, n, warnings);
     } catch (Exception e) {
       error(path, where.get("path"), e.getMessage(), IssueType.INVALID);
     }

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/sql/SQLOnFhirTests.java

@@ -83,23 +83,21 @@ public class SQLOnFhirTests {
       this.resources = resources;
       this.testCase = testCase;
     }
-
   }
 
   public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
     List<Arguments> objects = new ArrayList<>();
-    File dir = ManagedFileAccess.file("/Users/grahamegrieve/work/sql-on-fhir-v2/tests/content");
+    JsonArray testFiles = (JsonArray) JsonParser.parse(TestingUtilities.loadTestResourceStream("sql-on-fhir", "manifest.json"));
-    for (File f : dir.listFiles()) {
+
-      if (f.getName().endsWith(".json")) {
+    for (String s : testFiles.asStrings()) {
-        JsonObject json = JsonParser.parseObject(f);
+      JsonObject json = JsonParser.parseObject(TestingUtilities.loadTestResourceStream("sql-on-fhir", s));
-        String name1 = f.getName().replace(".json", "");
+      String name1 = s.replace(".json", "");
-        List<JsonObject> resources = json.getJsonObjects("resources");
+      List<JsonObject> resources = json.getJsonObjects("resources");
-        int i = 0;
+      int i = 0;
-        for (JsonObject test : json.getJsonObjects("tests")) {
+      for (JsonObject test : json.getJsonObjects("tests")) {
-          String name2 = test.asString("title");
+        String name2 = test.asString("title");
-          objects.add(Arguments.of(name1+":"+name2, new TestDetails(name1+":"+name2, "$.tests["+i+"]", resources, test)));
+        objects.add(Arguments.of(name1+":"+name2, new TestDetails(name1+":"+name2, "$.tests["+i+"]", resources, test)));
-          i++;
+        i++;
-        }
       }
     }
     return objects.stream();
@@ -110,7 +108,6 @@ public class SQLOnFhirTests {
   @SuppressWarnings("deprecation")
   @ParameterizedTest(name = "{index}: file {0}")
   @MethodSource("data")
-  @Disabled
   public void test(String name, TestDetails test) throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException, UcumException {
     this.details = test;
     Runner runner = new Runner();
@@ -137,8 +134,8 @@ public class SQLOnFhirTests {
         rows.add("rows", results);
         JsonObject exp = new JsonObject();
         exp.add("rows", test.testCase.getJsonArray("expect"));
-        sortResults(exp);
+//        sortResults(exp);
-        sortResults(rows);
+//        sortResults(rows);
         String expS = JsonParser.compose(exp, true);
         String rowS = JsonParser.compose(rows, true);
         String c = CompareUtilities.checkJsonSrcIsSame(name, expS, rowS, null);

org.hl7.fhir.report/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.3.24-SNAPSHOT</version>
+        <version>6.3.26-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.utilities/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.3.24-SNAPSHOT</version>
+        <version>6.3.26-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java

@@ -1491,7 +1491,7 @@ public class Utilities {
   }
 
   public static boolean startsWithInList(String s, Collection<String> list) {
-    if (s == null) {
+    if (s == null || list == null) {
       return false;
     }
     for (String l : list) {
@@ -1819,9 +1819,14 @@ public class Utilities {
 
   private static Object applyDatePrecision(String v, int precision) {
     switch (precision) {
-    case 4: return v.substring(0, 4);
+    case 4: 
-    case 6: return v.substring(0, 7);
+      return v.substring(0, 4);
-    case 8: return v.substring(0, 10);
+    case 6:
+    case 7:
+      return v.substring(0, 7);
+    case 8:
+    case 10:
+      return v.substring(0, 10);
     case 14: return v.substring(0, 17);
     case 17: return v;      
     }
@@ -2304,4 +2309,16 @@ public class Utilities {
     }
   }
 
+  public static boolean listValueStartsWith(String s, Set<String> list) {
+    if (s == null || list == null) {
+      return false;
+    }
+    for (String l : list) {
+      if (l.startsWith(s)) {
+        return true;
+      }
+    }
+    return false;
+  }
+
 }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java

@@ -210,26 +210,30 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
         Utilities.createDirectory(cacheFolder.getAbsolutePath());
         createIniFile();
       } else {
-        if (!isCacheFolderValid()) {
+        if (!iniFileExists()) {
+          createIniFile();
+        }
+        if (!isIniFileCurrentVersion()) {
           clearCache();
           createIniFile();
-        } else {
-          deleteOldTempDirectories();
         }
+        deleteOldTempDirectories();
       }
       return null;
     });
   }
 
-  private boolean isCacheFolderValid() throws IOException {
+  private boolean iniFileExists() throws IOException {
     String iniPath = getPackagesIniPath();
     File iniFile = ManagedFileAccess.file(iniPath);
-    if (!(iniFile.exists())) {
+    return iniFile.exists();
-      return false;
+  }
-    }
+
+  private boolean isIniFileCurrentVersion() throws IOException {
+    String iniPath = getPackagesIniPath();
     IniFile ini = new IniFile(iniPath);
-    String v = ini.getStringProperty("cache", "version");
+    String version = ini.getStringProperty("cache", "version");
-    return CACHE_VERSION.equals(v);
+    return CACHE_VERSION.equals(version);
   }
 
   private void deleteOldTempDirectories() throws IOException {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java

@@ -237,9 +237,11 @@ public class NpmPackage {
     public List<String> listFiles() {
       List<String> res = new ArrayList<>();
       if (folder != null) {
-        for (File f : folder.listFiles()) {
+        if (folder.exists()) {
-          if (!f.isDirectory() && !Utilities.existsInList(f.getName(), "package.json", ".index.json", ".index.db", ".oids.json", ".oids.db")) {
+          for (File f : folder.listFiles()) {
-            res.add(f.getName());
+            if (!f.isDirectory() && !Utilities.existsInList(f.getName(), "package.json", ".index.json", ".index.db", ".oids.json", ".oids.db")) {
+              res.add(f.getName());
+            }
           }
         }
       } else {
@@ -648,7 +650,17 @@ public class NpmPackage {
   }
 
 
-
+  /**
+   * Create a package .index.json file for a package folder.
+   * <p>
+   * See <a href="https://hl7.org/fhir/packages.html#2.1.10.4">the FHIR specification</a> for details on .index.json
+   * format and usage.
+   *
+   * @param desc
+   * @param folder
+   * @throws FileNotFoundException
+   * @throws IOException
+   */
   public void indexFolder(String desc, NpmPackageFolder folder) throws FileNotFoundException, IOException {
     List<String> remove = new ArrayList<>();
     NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageHacker.java

@@ -31,18 +31,19 @@ public class PackageHacker {
 
   public static void main(String[] args) throws FileNotFoundException, IOException {
 //    new PackageHacker().massEdit(new File("/Users/grahamegrieve/web/hl7.org/fhir"));
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.core.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.core.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.corexml.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.corexml.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.examples.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.examples.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.expansions.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.expansions.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.search.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot1/hl7.fhir.r6.search.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.core.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.core.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.corexml.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.corexml.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.examples.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.examples.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.expansions.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.expansions.tgz");
-    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.search.tgz");
+//    new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/6.0.0-ballot2/hl7.fhir.r6.search.tgz");
     
-//        new PackageHacker().edit(args[0]);
+//      new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/us/core/v311/package.tgz", "http://hl7.org/fhir/us/core/STU3.1.1");
+      new PackageHacker().edit("/Users/grahamegrieve/web/hl7.org/fhir/us/core/v700/package.tgz", "http://hl7.org/fhir/us/core/STU7");
   }
 
 //  private void massEdit(File dir) throws IOException {
@@ -91,7 +92,7 @@ public class PackageHacker {
 //    }
 //  }
 
-  private void edit(String name) throws FileNotFoundException, IOException {
+  private void edit(String name, String path) throws FileNotFoundException, IOException {
     File f = ManagedFileAccess.file(name);
     if (!f.exists())
       throw new Error("Unable to find "+f.getAbsolutePath());
@@ -107,15 +108,15 @@ public class PackageHacker {
     System.out.println("Altering Package "+f.getAbsolutePath());
     System.out.println(nice(pck.getNpm()));
 
-    if (change(pck.getNpm())) {
+    if (change(pck.getNpm(), path)) {
 
     System.out.println("Revised Package");
     System.out.println("=======================");
     System.out.println(nice(pck.getNpm()));
     System.out.println("=======================");
-//    System.out.print("save? y/n: ");
+    System.out.print("save? y/n: ");
-//    int r = System.in.read();
+    int r = System.in.read();
-//    if (r == 'y') {
+    if (r == 'y') {
       f.renameTo(ManagedFileAccess.file(Utilities.changeFileExt(name, ".tgz.bak")));
       FileOutputStream fso = ManagedFileAccess.outStream(f);
       try {
@@ -123,7 +124,7 @@ public class PackageHacker {
       } finally {
         fso.close();
       }
-//    } 
+    } 
     }
   }
 
@@ -142,13 +143,15 @@ public class PackageHacker {
     return JsonParser.compose(json, true);
   }
 
-  private boolean change(JsonObject npm) throws FileNotFoundException, IOException {
+  private boolean change(JsonObject npm, String path) throws FileNotFoundException, IOException {
-    //    fixVersions(npm, ver);
+    npm.remove("url");
-    if (npm.has("notForPublication")) {
+    npm.add("url", path);
-      npm.remove("notForPublication");
+    return true;
-      return true;
+//    if (npm.has("notForPublication")) {
-    }
+//      npm.remove("notForPublication");
-    return false;
+//      return true;
+//    }
+//    return false;
   }
 
   private void fixVersionInContent(Map<String, byte[]> content) {

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/npm/FilesystemPackageManagerTests.java

@@ -1,22 +1,25 @@
 package org.hl7.fhir.utilities.npm;
 
+import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 import java.io.File;
 
+import java.io.FileWriter;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Random;
+import java.util.UUID;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Stream;
 
 import javax.annotation.Nonnull;
 
+import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
-import org.junit.jupiter.api.RepeatedTest;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.condition.DisabledOnOs;
 import org.junit.jupiter.api.condition.EnabledOnOs;
@@ -100,7 +103,6 @@ public class FilesystemPackageManagerTests {
   @DisabledOnOs(OS.WINDOWS)
   public void testSystemCacheDirectory() throws IOException {
     File folder = new FilesystemPackageCacheManager.Builder().withSystemCacheFolder().getCacheFolder();
-
     assertEquals( "/var/lib/.fhir/packages", folder.getAbsolutePath());
   }
 
@@ -124,6 +126,118 @@ public class FilesystemPackageManagerTests {
     return params.stream();
   }
 
+  private void createDummyTemp(File cacheDirectory, String lowerCase) throws IOException {
+    createDummyPackage(cacheDirectory, lowerCase);
+  }
+
+  private void createDummyPackage(File cacheDirectory, String packageName, String packageVersion) throws IOException {
+    String directoryName = packageName + "#" + packageVersion;
+    createDummyPackage(cacheDirectory, directoryName);
+  }
+
+  private static void createDummyPackage(File cacheDirectory, String directoryName) throws IOException {
+    File packageDirectory = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), directoryName);
+    packageDirectory.mkdirs();
+
+    File dummyContentFile = ManagedFileAccess.file(packageDirectory.getAbsolutePath(), "dummy.txt");
+    FileWriter wr = new FileWriter(dummyContentFile);
+    wr.write("Ain't nobody here but us chickens");
+    wr.flush();
+    wr.close();
+  }
+
+  private void assertThatDummyTempExists(File cacheDirectory, String dummyTempPackage) throws IOException {
+    File dummyTempDirectory = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), dummyTempPackage);
+    assertThat(dummyTempDirectory).exists();
+
+    File dummyContentFile = ManagedFileAccess.file(dummyTempDirectory.getAbsolutePath(), "dummy.txt");
+    assertThat(dummyContentFile).exists();
+  }
+
+  @Test
+  public void testCreatesIniIfDoesntExistAndCacheStaysIntact() throws IOException {
+    File cacheDirectory = ManagedFileAccess.fromPath(Files.createTempDirectory("fpcm-multithreadingTest"));
+    File cacheIni = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini");
+
+    createDummyPackage(cacheDirectory, "example.fhir.uv.myig", "1.2.3");
+
+    String dummyTempPackage = UUID.randomUUID().toString().toLowerCase();
+    createDummyTemp(cacheDirectory, dummyTempPackage);
+    assertThatDummyTempExists(cacheDirectory, dummyTempPackage);
+
+    assertThat(cacheIni).doesNotExist();
+    FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager.Builder().withCacheFolder(cacheDirectory.getAbsolutePath()).build();
+    assertInitializedTestCacheIsValid(cacheDirectory, true);
+  }
+
+
+
+  @Test
+  public void testClearsCacheIfVersionIsWrong() throws IOException {
+    File cacheDirectory = ManagedFileAccess.fromPath(Files.createTempDirectory("fpcm-multithreadingTest"));
+    File cacheIni = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini");
+
+    createDummyPackage(cacheDirectory, "example.fhir.uv.myig", "1.2.3");
+    String dummyTempPackage = UUID.randomUUID().toString().toLowerCase();
+    createDummyTemp(cacheDirectory, dummyTempPackage);
+    assertThatDummyTempExists(cacheDirectory, dummyTempPackage);
+
+
+    IniFile ini = new IniFile(cacheIni.getAbsolutePath());
+    ini.setStringProperty("cache", "version", "2", null);
+    ini.save();
+
+    assertThat(cacheIni).exists();
+    FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager.Builder().withCacheFolder(cacheDirectory.getAbsolutePath()).build();
+    assertInitializedTestCacheIsValid(cacheDirectory, false);
+  }
+
+  @Test
+  public void testCacheStaysIntactIfVersionIsTheSame() throws IOException {
+    File cacheDirectory = ManagedFileAccess.fromPath(Files.createTempDirectory("fpcm-multithreadingTest"));
+    File cacheIni = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini");
+
+    createDummyPackage(cacheDirectory, "example.fhir.uv.myig", "1.2.3");
+    String dummyTempPackage = UUID.randomUUID().toString().toLowerCase();
+    createDummyTemp(cacheDirectory, dummyTempPackage);
+    assertThatDummyTempExists(cacheDirectory, dummyTempPackage);
+
+
+    IniFile ini = new IniFile(cacheIni.getAbsolutePath());
+    ini.setStringProperty("cache", "version", "3", null);
+    ini.save();
+
+    assertThat(cacheIni).exists();
+    FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager.Builder().withCacheFolder(cacheDirectory.getAbsolutePath()).build();
+    assertInitializedTestCacheIsValid(cacheDirectory, true);
+  }
+
+  private void assertInitializedTestCacheIsValid(File cacheDirectory, boolean dummyPackageShouldExist) throws IOException {
+    assertThat(cacheDirectory).exists();
+    File iniFile = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini");
+    assertThat(ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini")).exists();
+    IniFile ini = new IniFile(iniFile.getAbsolutePath());
+    String version = ini.getStringProperty("cache", "version");
+    assertThat(version).isEqualTo("3");
+
+    File[] files = cacheDirectory.listFiles();
+    if (dummyPackageShouldExist) {
+      // Check that only packages.ini and our dummy package are in the cache. Our previous temp should be deleted.
+      assertThat(files).hasSize(2); // packages.ini and example.fhir.uv.myig#1.2.3 (directory)
+
+      File dummyPackage = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "example.fhir.uv.myig#1.2.3");
+      assertThat(dummyPackage).exists();
+
+      File dummyContentFile = ManagedFileAccess.file(dummyPackage.getAbsolutePath(), "dummy.txt");
+      assertThat(dummyContentFile).exists();
+    } else {
+      // Check that only packages.ini is in the cache.
+      assertThat(files).hasSize(1);
+    }
+
+
+  }
+
   @MethodSource("packageCacheMultiThreadTestParams")
   @ParameterizedTest
   public void packageCacheMultiThreadTest(final int threadTotal, final int packageCacheManagerTotal) throws IOException {

org.hl7.fhir.validation.cli/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.3.24-SNAPSHOT</version>
+        <version>6.3.26-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.validation/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.3.24-SNAPSHOT</version>
+        <version>6.3.26-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -119,37 +119,6 @@
             <optional>true</optional>
         </dependency>
 
-        <!-- CQL-to-ELM -->
-        <dependency>
-            <groupId>info.cqframework</groupId>
-            <artifactId>cql</artifactId>
-            <version>${info_cqframework_version}</version>
-        </dependency>
-        <dependency>
-            <groupId>info.cqframework</groupId>
-            <artifactId>model</artifactId>
-            <version>${info_cqframework_version}</version>
-        </dependency>
-        <dependency>
-            <groupId>info.cqframework</groupId>
-            <artifactId>elm</artifactId>
-            <version>${info_cqframework_version}</version>
-        </dependency>
-        <dependency>
-            <groupId>info.cqframework</groupId>
-            <artifactId>cql-to-elm</artifactId>
-            <version>${info_cqframework_version}</version>
-        </dependency>
-        <dependency>
-            <groupId>info.cqframework</groupId>
-            <artifactId>quick</artifactId>
-            <version>${info_cqframework_version}</version>
-        </dependency>
-        <dependency>
-            <groupId>info.cqframework</groupId>
-            <artifactId>qdm</artifactId>
-            <version>${info_cqframework_version}</version>
-        </dependency>
         <!-- OkHttpDependency -->
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java

@@ -226,6 +226,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
   @Getter @Setter private boolean allowDoubleQuotesInFHIRPath;
   @Getter @Setter private boolean checkIPSCodes;
   @Getter @Setter private BestPracticeWarningLevel bestPracticeLevel;
+  @Getter @Setter private boolean unknownCodeSystemsCauseErrors;
   @Getter @Setter private Locale locale;
   @Getter @Setter private List<ImplementationGuide> igs = new ArrayList<>();
   @Getter @Setter private List<String> extensionDomains = new ArrayList<>();
@@ -289,6 +290,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
     fhirPathEngine = other.fhirPathEngine;
     igLoader = other.igLoader;
     jurisdiction = other.jurisdiction;
+    unknownCodeSystemsCauseErrors = other.unknownCodeSystemsCauseErrors;
   }
   
   /**
@@ -906,6 +908,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
     if (policyAdvisor != null) {
       validator.setPolicyAdvisor(policyAdvisor);
     }
+    validator.setUnknownCodeSystemsCauseErrors(unknownCodeSystemsCauseErrors);
     return validator;
   }
 

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/CliContext.java

@@ -163,6 +163,9 @@ public class CliContext {
   @JsonProperty("bestPracticeLevel")
   private BestPracticeWarningLevel bestPracticeLevel = BestPracticeWarningLevel.Warning;
 
+  @JsonProperty("unknownCodeSystemsCauseErrors")
+  private boolean unknownCodeSystemsCauseErrors;
+  
   @JsonProperty("baseEngine")
   public String getBaseEngine() {
     return baseEngine;
@@ -832,6 +835,7 @@ public class CliContext {
       Objects.equals(watchMode, that.watchMode) &&
       Objects.equals(bestPracticeLevel, that.bestPracticeLevel) &&
       Objects.equals(watchScanDelay, that.watchScanDelay) &&
+      Objects.equals(unknownCodeSystemsCauseErrors, that.unknownCodeSystemsCauseErrors) &&
       Objects.equals(watchSettleTime, that.watchSettleTime) ;
   }
 
@@ -839,8 +843,8 @@ public class CliContext {
   public int hashCode() {
     return Objects.hash(baseEngine, doNative, extensions, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching,
             noExtensibleBindingMessages, noInvariants, displayWarnings, wantInvariantsInMessages, map, output, outputSuffix, htmlOutput, txServer, sv, txLog, txCache, mapLog, lang, srcLang, tgtLang, fhirpath, snomedCT,
-            targetVer, igs, questionnaireMode, level, profiles, sources, inputs, mode, locale, locations, crumbTrails, forPublication, showTimes, allowExampleUrls, outputStyle, jurisdiction, noUnicodeBiDiControlChars, watchMode, watchScanDelay, watchSettleTime, bestPracticeLevel,
+            targetVer, igs, questionnaireMode, level, profiles, sources, inputs, mode, locale, locations, crumbTrails, forPublication, showTimes, allowExampleUrls, outputStyle, jurisdiction, noUnicodeBiDiControlChars,
-            htmlInMarkdownCheck, allowDoubleQuotesInFHIRPath, checkIPSCodes);
+            watchMode, watchScanDelay, watchSettleTime, bestPracticeLevel, unknownCodeSystemsCauseErrors, htmlInMarkdownCheck, allowDoubleQuotesInFHIRPath, checkIPSCodes);
   }
 
   @Override
@@ -899,6 +903,7 @@ public class CliContext {
       ", bestPracticeLevel=" + bestPracticeLevel +
       ", watchSettleTime=" + watchSettleTime +
       ", watchScanDelay=" + watchScanDelay +
+      ", unknownCodeSystemsCauseErrors=" + unknownCodeSystemsCauseErrors +
       '}';
   }
 
@@ -956,4 +961,17 @@ public class CliContext {
     return this;
   }
 
+
+  @JsonProperty("unknownCodeSystemsCauseErrors")
+  public boolean isUnknownCodeSystemsCauseErrors() {
+    return unknownCodeSystemsCauseErrors;
+  }
+
+
+  @JsonProperty("unknownCodeSystemsCauseErrors")
+  public void setUnknownCodeSystemsCauseErrors(boolean unknownCodeSystemsCauseErrors) {
+    this.unknownCodeSystemsCauseErrors = unknownCodeSystemsCauseErrors;
+  }
+
+  
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java

@@ -581,6 +581,7 @@ public class ValidationService {
     }
     validationEngine.getBundleValidationRules().addAll(cliContext.getBundleValidationRules());
     validationEngine.setJurisdiction(CodeSystemUtilities.readCoding(cliContext.getJurisdiction()));
+    validationEngine.setUnknownCodeSystemsCauseErrors(cliContext.isUnknownCodeSystemsCauseErrors());
     TerminologyCache.setNoCaching(cliContext.isNoInternalCaching());
     validationEngine.prepare(); // generate any missing snapshots
     System.out.println(" go (" + timeTracker.milestone() + ")");

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java

@@ -94,8 +94,7 @@ public class Params {
   public static final String DISABLE_DEFAULT_RESOURCE_FETCHER = "-disable-default-resource-fetcher";
   public static final String CHECK_IPS_CODES = "-check-ips-codes";
   public static final String BEST_PRACTICE = "-best-practice";
-  
+  public static final String UNKNOWN_CODESYSTEMS_CAUSE_ERROR = "-unknown-codesystems-cause-errors";  
-  
 
   public static final String RUN_TESTS = "-run-tests";
 
@@ -320,6 +319,8 @@ public class Params {
         cliContext.setCrumbTrails(true);
       } else if (args[i].equals(FOR_PUBLICATION)) {
         cliContext.setForPublication(true);
+      } else if (args[i].equals(UNKNOWN_CODESYSTEMS_CAUSE_ERROR)) {
+        cliContext.setUnknownCodeSystemsCauseErrors(true);
       } else if (args[i].equals(VERBOSE)) {
         cliContext.setCrumbTrails(true);
       } else if (args[i].equals(ALLOW_EXAMPLE_URLS)) {

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

@@ -46,7 +46,7 @@ import javax.annotation.Nonnull;
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.fhir.ucum.Decimal;
-import org.hl7.elm.r1.Code;
+
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.PathEngineException;
@@ -598,6 +598,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   private boolean example ;
   private IDigitalSignatureServices signatureServices;
   private ContextUtilities cu;
+  private boolean unknownCodeSystemsCauseErrors;
 
   public InstanceValidator(@Nonnull IWorkerContext theContext, @Nonnull IEvaluationContext hostServices, @Nonnull XVerExtensionManager xverManager) {
     super(theContext, xverManager, false);
@@ -1125,7 +1126,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       timeTracker.tx(t, "vc "+system+"#"+code+" '"+display+"'");
       if (s == null)
         return true;
-      ok = processTxIssues(errors, s, element, path, null, "no binding on code", false, null) & ok;
+      ok = processTxIssues(errors, s, element, path, false, null, null) & ok;
 
       if (s.isOk()) {
         if (s.getMessage() != null && !s.messageIsInIssues()) {
@@ -1381,7 +1382,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         if (cc.hasCoding()) {
           long t = System.nanoTime();
           ValidationResult vr = checkCodeOnServer(stack, null, cc);
-          bh.see(processTxIssues(errors, vr, element, path, org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.INFORMATION, null, false, null));
+          bh.see(processTxIssues(errors, vr, element, path, false, null, null));
           timeTracker.tx(t, "vc " + cc.toString());
         }
       } catch (CheckCodeOnServerException e) {
@@ -1465,7 +1466,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
           } else {
             checked.set(true);
             ValidationResult vr = checkCodeOnServer(stack, valueset, cc);
-            bh.see(processTxIssues(errors, vr, element, path, notFoundSeverityForBinding(strength), notFoundSeverityNoteForBinding(strength), false, vsRef));
+            bh.see(processTxIssues(errors, vr, element, path, false, vsRef, strength));
             if (!vr.isOk()) {
               bindingsOk = false;
               if (vr.getErrorClass() != null && vr.getErrorClass() == TerminologyServiceErrorClass.NOSERVICE) { 
@@ -1533,33 +1534,34 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return checkDisp;
   }
 
-  private String notFoundSeverityNoteForBinding(BindingStrength strength) {
+//  private String notFoundSeverityNoteForBinding(BindingStrength strength, Set<String> systems) {
-    if (strength == BindingStrength.REQUIRED) {
+//    if (strength == BindingStrength.REQUIRED && 
-      return "error because this is a required binding";
+//        (Utilities.listValueStartsWith("http://hl7.org/fhir", systems) || Utilities.listValueStartsWith("http://terminology.hl7.org", systems))) {
-    } else {
+//      return "error because this is a required binding to an HL7 code system";
-      return null;     
+//    } else {
-    }
+//      return null;     
-  }
+//    }
+//  }
+//
+//  /**
+//   * The terminology server will report an error for an unknown code system or version, or a dependent valueset
+//   * 
+//   * but we only care for validation if the binding strength is strong enough. 
+//   * @param binding
+//   * @return
+//   */
+//  private org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity notFoundSeverityForBinding(BindingStrength strength, String systems) {
+//    if (strength == BindingStrength.REQUIRED && 
+//        (Utilities.listValueStartsWith("http://hl7.org/fhir", systems) || Utilities.listValueStartsWith("http://terminology.hl7.org", systems))) {
+//      return org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.ERROR;
+//    } else if (strength == BindingStrength.REQUIRED || strength == BindingStrength.EXTENSIBLE) {
+//      return org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.WARNING;
+//    } else {
+//      return org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.INFORMATION;      
+//    }
+//  }
 
-  /**
+  private boolean processTxIssues(List<ValidationMessage> errors, ValidationResult vr, Element element, String path, boolean ignoreCantInfer, String vsurl, BindingStrength bs) {
-   * The terminology server will report an error for an unknown code system or version, or a dependent valueset
-   * 
-   * but we only care for validation if the binding strength is strong enough. 
-   * @param binding
-   * @return
-   */
-  private org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity notFoundSeverityForBinding(BindingStrength strength) {
-    if (strength == BindingStrength.REQUIRED) {
-      return org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.ERROR;
-    } else if (strength == BindingStrength.EXTENSIBLE) {
-      return org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.WARNING;
-    } else {
-      return org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.INFORMATION;      
-    }
-  }
-
-  private boolean processTxIssues(List<ValidationMessage> errors, ValidationResult vr, Element element, String path, 
-      org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity notFoundLevel, String notFoundNote, boolean ignoreCantInfer, String vsurl) {
     boolean ok = true;
     if (vr != null) {
       for (OperationOutcomeIssueComponent iss : vr.getIssues()) {
@@ -1567,12 +1569,35 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             && !iss.getDetails().hasCoding("http://hl7.org/fhir/tools/CodeSystem/tx-issue-type", "this-code-not-in-vs")
             && !(ignoreCantInfer || iss.getDetails().hasCoding("http://hl7.org/fhir/tools/CodeSystem/tx-issue-type", "cannot-infer"))) {
           OperationOutcomeIssueComponent i = iss.copy();
-          if (i.getDetails().hasCoding("http://hl7.org/fhir/tools/CodeSystem/tx-issue-type", "not-found")) { 
+          if (i.getDetails().hasCoding("http://hl7.org/fhir/tools/CodeSystem/tx-issue-type", "not-found")) {
-            if (notFoundLevel != null && i.getSeverity().isHigherThan(notFoundLevel) || (vsurl != null && i.getDetails().getText().contains(vsurl))) {
+            String msg = iss.getDetails().getText();
-              i.setSeverity(notFoundLevel);
+            boolean isHL7 = msg == null ? false : msg.contains("http://hl7.org/fhir") || msg.contains("http://terminology.hl7.org");
+            org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity notFoundLevel = null;
+            String notFoundNote = null;
+            if (bs == null) {
+              notFoundLevel = org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.WARNING;
+              notFoundNote = null; // "binding=null";
+            } else if (bs == BindingStrength.REQUIRED && isHL7) {
+              notFoundLevel = org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.ERROR;
+              notFoundNote = "error because this is a required binding to an HL7 code system";
+            } else if (bs == BindingStrength.REQUIRED && unknownCodeSystemsCauseErrors) {
+              notFoundLevel = org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.ERROR;
+              notFoundNote = "error because this is a required binding";              
+            } else if (bs == BindingStrength.REQUIRED) {
+              notFoundLevel = org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.WARNING;
+              notFoundNote = null; // "binding=required";              
+            } else if (bs == BindingStrength.EXTENSIBLE) {
+              notFoundLevel = org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.WARNING;
+              notFoundNote = null; // "binding=extensible";
+            } else {
+              notFoundLevel = org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.WARNING;
+              notFoundNote = null; // "binding="+bs.toCode();
             }
-            if (notFoundNote != null) {
+            if (notFoundLevel != null && i.getSeverity().isHigherThan(notFoundLevel)) { // && (vsurl != null && i.getDetails().getText().contains(vsurl))) {
-              i.getDetails().setText(i.getDetails().getText()+" ("+notFoundNote+")");
+              i.setSeverity(notFoundLevel);
+              if (notFoundNote != null) {
+                i.getDetails().setText(i.getDetails().getText()+" ("+notFoundNote+")");
+              }
             }
           }
           if (baseOptions.isDisplayWarningMode() && i.getSeverity() == org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.ERROR && i.getDetails().hasCoding("http://hl7.org/fhir/tools/CodeSystem/tx-issue-type", "invalid-display")) {
@@ -1592,7 +1617,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     boolean ok = true;
     if (isNotBlank(nextCoding.getCode()) && isNotBlank(nextCoding.getSystem()) && context.supportsSystem(nextCoding.getSystem(), baseOptions.getFhirVersion())) {
       ValidationResult vr = checkCodeOnServer(stack, valueset, nextCoding);
-      ok = processTxIssues(errors, vr, element, path, null, "ex-checkBindings", false, null) && ok;
+      ok = processTxIssues(errors, vr, element, path, false, null, null) && ok;
 
       if (vr.getSeverity() != null && !vr.messageIsInIssues()) {
         if (vr.getSeverity() == IssueSeverity.INFORMATION) {
@@ -1721,7 +1746,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         if (strength == BindingStrength.REQUIRED) {
           removeTrackedMessagesForLocation(errors, element, path);
         }
-        ok = processTxIssues(errors, vr, element, path, notFoundSeverityForBinding(strength), notFoundSeverityNoteForBinding(strength), false, vsRef) && ok;
+        ok = processTxIssues(errors, vr, element, path, false, vsRef, strength) && ok;
         timeTracker.tx(t, "vc "+system+"#"+code+" '"+display+"'");
         if (vr != null && !vr.isOk()) {
           if (vr.IsNoService())
@@ -1766,6 +1791,21 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return ok;
   }
 
+  private Set<String> getUnknownSystems(ValidationResult vr) {
+    if (vr == null) {
+      return null;
+    }
+    if (vr.getUnknownSystems() != null && !vr.getUnknownSystems().isEmpty()) {
+      return vr.getUnknownSystems();
+    }
+    if (vr.getSystem() != null) {
+      Set<String> set = new HashSet<String>();
+      set.add(vr.getSystem());
+      return set;
+    }
+    return null;
+  }
+
   private boolean convertCDACodeToCodeableConcept(List<ValidationMessage> errors, String path, Element element, StructureDefinition logical, CodeableConcept cc) {
     boolean ok = true;
     cc.setText(element.getNamedChildValue("originalText", false));
@@ -1851,7 +1891,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       try {
         long t = System.nanoTime();
         ValidationResult vr = checkCodeOnServer(stack, valueset, cc);
-        ok = processTxIssues(errors, vr, element, path, null, "ex-checkMaxValueSet", false, maxVSUrl) && ok;
+        ok = processTxIssues(errors, vr, element, path, false, maxVSUrl, null) && ok;
         timeTracker.tx(t, "vc "+cc.toString());
         if (!vr.isOk()) {
           if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure())
@@ -1890,7 +1930,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       try {
         long t = System.nanoTime();
         ValidationResult vr = checkCodeOnServer(stack, valueset, c);
-        ok = processTxIssues(errors, vr, element, path, null, "ex-checkMaxValueSet-2", false, maxVSUrl) && ok;
+        ok = processTxIssues(errors, vr, element, path, false, maxVSUrl, null) && ok;
 
         timeTracker.tx(t, "vc "+c.getSystem()+"#"+c.getCode()+" '"+c.getDisplay()+"'");
         if (!vr.isOk()) {
@@ -1921,7 +1961,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       try {
         long t = System.nanoTime();
         ValidationResult vr = checkCodeOnServer(stack, valueset, value, baseOptions);
-        ok = processTxIssues(errors, vr, element, path, null, "ex-checkMaxValueSet-3", false, maxVSUrl) && ok;
+        ok = processTxIssues(errors, vr, element, path, false, maxVSUrl, null) && ok;
         timeTracker.tx(t, "vc "+value);
         if (!vr.isOk()) {
           if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure())
@@ -2045,7 +2085,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         checked.set(true);
         vr = checkCodeOnServer(stack, valueset, c);
       }
-      ok = processTxIssues(errors, vr, element, path, notFoundSeverityForBinding(strength), notFoundSeverityNoteForBinding(strength), strength == BindingStrength.EXTENSIBLE, vsRef) && ok;
+      ok = processTxIssues(errors, vr, element, path, strength == BindingStrength.EXTENSIBLE, vsRef, strength) && ok;
 
       timeTracker.tx(t, "vc "+c.getSystem()+"#"+c.getCode()+" '"+c.getDisplay()+"'");
       if (strength == BindingStrength.REQUIRED) {
@@ -3510,7 +3550,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             }
             vr = checkCodeOnServer(stack, vs, value, options);
           }
-          ok = processTxIssues(errors, vr, element, path, notFoundSeverityForBinding(binding.getStrength()), notFoundSeverityNoteForBinding(binding.getStrength()), binding.getStrength() != BindingStrength.REQUIRED, binding.getValueSet()) && ok;
+          ok = processTxIssues(errors, vr, element, path, binding.getStrength() != BindingStrength.REQUIRED, binding.getValueSet(), binding.getStrength()) && ok;
 
           timeTracker.tx(t, "vc "+value+"");
           if (binding.getStrength() == BindingStrength.REQUIRED) {
@@ -7791,4 +7831,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     this.fetcher = value;
     return this;
   }
+
+  public boolean isUnknownCodeSystemsCauseErrors() {
+    return unknownCodeSystemsCauseErrors;
+  }
+
+  public void setUnknownCodeSystemsCauseErrors(boolean unknownCodeSystemsCauseErrors) {
+    this.unknownCodeSystemsCauseErrors = unknownCodeSystemsCauseErrors;
+  }
+  
+  
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/FHIRPathExpressionFixer.java

@@ -61,7 +61,7 @@ public class FHIRPathExpressionFixer {
     }
     // con-3 in R4
     if (expr.equals("clinicalStatus.exists() or verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() or category.select($this='problem-list-item').empty()")) {
-      return "clinicalStatus.exists() or verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() or category.coding.exists(system='http://terminology.hl7.org/CodeSystem/condition-category' and code ='problem-list-item').empty()";
+      return "(verificationStatus.coding.where(system='http://terminology.hl7.org/CodeSystem/condition-ver-status' and code = 'entered-in-error').exists() and category.coding.exists(system='http://terminology.hl7.org/CodeSystem/condition-category' and code ='problem-list-item').empty()) implies (clinicalStatus.exists())";
     }
     
     // R5 ballot

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxTesterSorters.java

@@ -8,10 +8,10 @@ import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 
-import org.hl7.fhir.ParametersParameter;
+
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonParser;
-import org.hl7.fhir.r5.model.Base;
+
 import org.hl7.fhir.r5.model.Extension;
 import org.hl7.fhir.r5.model.OperationOutcome;
 import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;

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

@@ -247,9 +247,9 @@ public class ValidationEngineTests {
     Assertions.assertTrue(checkOutcomes("testObs102", op, 
         "Observation.text.div null error/invalid: Wrong namespace on the XHTML ('null', should be 'http://www.w3.org/1999/xhtml')\n"+
         "Observation.category null information/business-rule: Reference to experimental CodeSystem http://hl7.org/fhir/observation-category\n"+
-        "Observation.code.coding[2].system null information/not-found: A definition for CodeSystem 'http://acme.org/devices/clinical-codes' could not be found, so the code cannot be validated\n"+
         "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
-        "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()"));
+        "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()\n"+
+        "Observation.code.coding[2].system null warning/not-found: A definition for CodeSystem 'http://acme.org/devices/clinical-codes' could not be found, so the code cannot be validated"));
     verifyNoTerminologyRequests(logger);
   }
 
@@ -265,8 +265,8 @@ public class ValidationEngineTests {
       System.out.println("  .. load USCore");
     OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "observation301.xml"), null);
     Assertions.assertTrue(checkOutcomes("test301", op,
-        "Observation.code.coding[3].system null information/not-found: A definition for CodeSystem 'http://acme.org/devices/clinical-codes' could not be found, so the code cannot be validated\n"+
+        "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
-        "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer"));
+        "Observation.code.coding[3].system null warning/not-found: A definition for CodeSystem 'http://acme.org/devices/clinical-codes' could not be found, so the code cannot be validated"));
     verifyNoTerminologyRequests(logger);
   }
 

pom.xml

@@ -14,14 +14,14 @@
     HAPI FHIR
     -->
     <artifactId>org.hl7.fhir.core</artifactId>
-    <version>6.3.24-SNAPSHOT</version>
+    <version>6.3.26-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <properties>
         <commons_compress_version>1.26.0</commons_compress_version>
         <guava_version>32.0.1-jre</guava_version>
         <hapi_fhir_version>6.4.1</hapi_fhir_version>
-        <validator_test_case_version>1.5.21-SNAPSHOT</validator_test_case_version>
+        <validator_test_case_version>1.5.22-SNAPSHOT</validator_test_case_version>
         <jackson_version>2.17.0</jackson_version>
         <junit_jupiter_version>5.9.2</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>