Merge branch 'master' into do-20240909-package-lock-cleanup

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

@@ -237,11 +237,13 @@ public class NpmPackage {
     public List<String> listFiles() {
       List<String> res = new ArrayList<>();
       if (folder != null) {
+        if (folder.exists()) {
           for (File f : folder.listFiles()) {
             if (!f.isDirectory() && !Utilities.existsInList(f.getName(), "package.json", ".index.json", ".index.db", ".oids.json", ".oids.db")) {
               res.add(f.getName());
             }
           }
+        }
       } else {
         for (String s : content.keySet()) {
           if (!Utilities.existsInList(s, "package.json", ".index.json", ".index.db", ".oids.json", ".oids.db")) {

org.hl7.fhir.validation/pom.xml

@@ -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/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;

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;

pom.xml

@@ -21,7 +21,7 @@
         <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</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>