Merge remote-tracking branch 'origin/master' into do-20230315-pathbuilder

org.hl7.fhir.convertors/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.113-SNAPSHOT</version>
+        <version>5.6.115-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/resources40_50/ImplementationGuide40_50.java

@@ -2350,7 +2350,7 @@ public class ImplementationGuide40_50 {
           tgt.addParameter(convertImplementationGuideDefinitionParameterComponent(t));
         } else {
           org.hl7.fhir.r4.model.Extension e = new org.hl7.fhir.r4.model.Extension(EXT_IG_DEFINITION_PARAMETER);
-          org.hl7.fhir.r4.model.Extension eCode = new org.hl7.fhir.r4.model.Extension("code", new org.hl7.fhir.r4.model.StringType(t.getCode().getCode()));
+          org.hl7.fhir.r4.model.Extension eCode = new org.hl7.fhir.r4.model.Extension("code", new org.hl7.fhir.r4.model.CodeType(t.getCode().getCode()));
           org.hl7.fhir.r4.model.Extension eValue = new org.hl7.fhir.r4.model.Extension("value", new org.hl7.fhir.r4.model.StringType(t.getValue()));
           e.addExtension(eCode);
           e.addExtension(eValue);

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv43_50/resources43_50/ImplementationGuide43_50.java

@@ -2344,7 +2344,7 @@ public class ImplementationGuide43_50 {
         tgt.addParameter(convertImplementationGuideDefinitionParameterComponent(t));
       else {
         org.hl7.fhir.r4b.model.Extension e = new org.hl7.fhir.r4b.model.Extension(EXT_IG_DEFINITION_PARAMETER);
-        org.hl7.fhir.r4b.model.Extension eCode = new org.hl7.fhir.r4b.model.Extension("code", new org.hl7.fhir.r4b.model.StringType(t.getCode().getCode()));
+        org.hl7.fhir.r4b.model.Extension eCode = new org.hl7.fhir.r4b.model.Extension("code", new org.hl7.fhir.r4b.model.CodeType(t.getCode().getCode()));
         org.hl7.fhir.r4b.model.Extension eValue = new org.hl7.fhir.r4b.model.Extension("value", new org.hl7.fhir.r4b.model.StringType(t.getValue()));
         e.addExtension(eCode);
         e.addExtension(eValue);

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/BaseLoaderR5.java

@@ -24,6 +24,7 @@ import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
 
 import com.google.gson.JsonSyntaxException;
 
@@ -40,6 +41,7 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
   @Getter @Setter protected boolean killPrimitives;
   @Getter protected List<String> types = new ArrayList<>();
   protected ILoaderKnowledgeProviderR5 lkp;
+  private boolean loadProfiles = true;
 
   public BaseLoaderR5(List<String> types, ILoaderKnowledgeProviderR5 lkp) {
     super();
@@ -169,6 +171,12 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
         String url = URL_BASE+versionString()+"/StructureDefinition/"+code;
         ToolingExtensions.setUrlExtension(tr, ToolingExtensions.EXT_FHIR_TYPE, url);
       }
+      for (CanonicalType c : tr.getProfile()) {
+        c.setValue(patchUrl(c.getValue(), "StructureDefinition"));
+      }
+      for (CanonicalType c : tr.getTargetProfile()) {
+        c.setValue(patchUrl(c.getValue(), "StructureDefinition"));
+      }
     }
     if (ed.hasBinding()) {
       ed.getBinding().setValueSet(patchUrl(ed.getBinding().getValueSet(), "ValueSet"));
@@ -178,4 +186,20 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
     }
   }
 
+  public IContextResourceLoader setLoadProfiles(boolean value) {
+    loadProfiles = value;
+    return this;
+  }
+  
+  public boolean wantLoad(NpmPackage pi, PackageResourceInformation pri) {
+    if (pri.getResourceType().equals("StructureDefinition")) {
+      if (loadProfiles) {
+        return true;
+      } else {
+        return pi.isCore() && Utilities.tail(pri.getUrl()).equals(pri.getStatedType());
+      }
+    } else {
+      return true;
+    }
+  }
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R4ToR5Loader.java

@@ -127,7 +127,7 @@ public class R4ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
     if (killPrimitives) {
       throw new FHIRException("Cannot kill primitives when using deferred loading");
     }
-    if (r5 instanceof StructureDefinition && VersionUtilities.isR4BVer(version)) {
+    if (r5 instanceof StructureDefinition && VersionUtilities.isR4Ver(version)) {
       r5 = new StructureDefinitionHacker(version).fixSD((StructureDefinition) r5);
     }
     if (patchUrls) {

org.hl7.fhir.dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.113-SNAPSHOT</version>
+		<version>5.6.115-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>5.6.113-SNAPSHOT</version>
+		<version>5.6.115-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>5.6.113-SNAPSHOT</version>
+        <version>5.6.115-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>5.6.113-SNAPSHOT</version>
+		<version>5.6.115-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>5.6.113-SNAPSHOT</version>
+		<version>5.6.115-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/test/utils/TestingUtilities.java

@@ -149,7 +149,7 @@ public class TestingUtilities extends BaseTestingUtilities {
 
   public static String checkXMLIsSame(String f1, String f2) throws Exception {
     String result = compareXml(f1, f2);
-    if (result != null && SHOW_DIFF) {
+    if (result != null && SHOW_DIFF && System.getenv("ProgramFiles") != null) {
       String diff = Utilities.path(System.getenv("ProgramFiles"), "WinMerge", "WinMergeU.exe");
       if (new File(diff).exists()) {
         List<String> command = new ArrayList<String>();

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.113-SNAPSHOT</version>
+		<version>5.6.115-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ProfileComparer.java

@@ -1154,7 +1154,7 @@ public boolean prependLinks() {
 
 @Override
 public String getLinkForUrl(String corePath, String s) {
-  throw new NotImplementedError();
+  return null;
 }
   
 

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

@@ -1,5 +1,6 @@
 package org.hl7.fhir.r5.conformance;
 
+import org.hl7.fhir.r5.model.CanonicalType;
 import org.hl7.fhir.r5.model.ElementDefinition;
 import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
 import org.hl7.fhir.r5.model.Resource;
@@ -22,8 +23,25 @@ public class StructureDefinitionHacker {
   }
 
   public Resource fixSD(StructureDefinition sd) {
+    if (VersionUtilities.isR4Ver(version) && "http://hl7.org/fhir/StructureDefinition/example-composition".equals(sd.getUrl())) {
+      for (ElementDefinition ed : sd.getSnapshot().getElement()) {
+        fixDocSecURL(ed);
+      } for (ElementDefinition ed : sd.getDifferential().getElement()) {
+        fixDocSecURL(ed);
+      }
+    }
     return sd;
   }
 
+  private void fixDocSecURL(ElementDefinition ed) {
+    for (TypeRefComponent tr : ed.getType()) {
+      for (CanonicalType c : tr.getProfile()) {
+        if ("http://hl7.org/fhir/StructureDefinition/document-section-library".equals(c.getValue())) {
+          c.setValue("http://hl7.org/fhir/StructureDefinition/example-section-library");
+        }
+      }
+    }
+  }
+
 
 }

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

@@ -661,10 +661,7 @@ public class ProfileUtilities extends TranslatingUtilities {
                 System.out.println("  "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+"  "+constraintSummary(ed));
             }
           }
-          if (exception)
+          handleError(url, msg);
-            throw new DefinitionException(msg);
-          else
-            messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
         }
         // hack around a problem in R4 definitions (somewhere?)
         for (ElementDefinition ed : derived.getSnapshot().getElement()) {
@@ -712,14 +709,20 @@ public class ProfileUtilities extends TranslatingUtilities {
                 if (ed.getPath().equals("Bundle.entry.response.outcome")) {
                   wt = "OperationOutcome";
                 }
-                if (!sd.getType().equals(wt)) {
+                String tt = sd.getType();
-                  boolean ok = isCompatibleType(wt, sd);
+                boolean elementProfile = u.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT);
+                if (elementProfile) {
+                  ElementDefinition edt = sd.getSnapshot().getElementById(u.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT));
+                  if (edt == null) {
+                    handleError(url, "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt);
+                  } else {
+                    tt = edt.typeSummary();
+                  }
+                }
+                if (!tt.equals(wt)) {
+                  boolean ok = !elementProfile && isCompatibleType(wt, sd);
                   if (!ok) {
-                    String smsg = "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt;
+                    handleError(url, "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt);
-                    if (exception)
-                      throw new DefinitionException(smsg);
-                    else
-                      messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), smsg, IssueSeverity.ERROR));
                   }
                 }
               }
@@ -738,6 +741,13 @@ public class ProfileUtilities extends TranslatingUtilities {
     }
   }
 
+  private void handleError(String url, String msg) {
+    if (exception)
+      throw new DefinitionException(msg);
+    else
+      messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
+  }
+
 
 
 
@@ -1973,7 +1983,8 @@ public class ProfileUtilities extends TranslatingUtilities {
       base.getAlias().addAll(e.getAlias());
       base.getMapping().clear();
       base.getMapping().addAll(e.getMapping());
-    } else if (source.getType().size() == 1 && source.getTypeFirstRep().hasProfile()) {
+    } else if (source.getType().size() == 1 && source.getTypeFirstRep().hasProfile() && !source.getTypeFirstRep().getProfile().get(0).hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT)) {
+      // todo: should we change down the profile_element if there's one?
       String type = source.getTypeFirstRep().getWorkingCode();
       if ("Extension".equals(type)) {
         System.out.println("Can't find Extension definition for "+source.getTypeFirstRep().getProfile().get(0).asStringValue()+" but trying to go on");          
@@ -2270,11 +2281,11 @@ public class ProfileUtilities extends TranslatingUtilities {
             t.setUserData(UD_DERIVATION_EQUALS, true);
       }
 
+      List<ElementDefinitionMappingComponent> list = new ArrayList<>();
+      list.addAll(base.getMapping());
+      base.getMapping().clear();
+      addMappings(base.getMapping(), list);
       if (derived.hasMapping()) {
-        List<ElementDefinitionMappingComponent> list = new ArrayList<>();
-        list.addAll(base.getMapping());
-        base.getMapping().clear();
-        addMappings(base.getMapping(), list);
         addMappings(base.getMapping(), derived.getMapping());
       } 
       for (ElementDefinitionMappingComponent m : base.getMapping()) {

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

@@ -793,6 +793,9 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     if (pIn == null) {
       throw new Error(formatMessage(I18nConstants.NO_PARAMETERS_PROVIDED_TO_EXPANDVS));
     }
+    if (vs.getUrl().equals("http://hl7.org/fhir/ValueSet/all-time-units") || vs.getUrl().equals("http://hl7.org/fhir/ValueSet/all-distance-units")) {
+      return new ValueSetExpansionOutcome("This value set is not expanded correctly at this time (will be fixed in a future version)", TerminologyServiceErrorClass.VALUESET_UNSUPPORTED);
+    }
     
     Parameters p = pIn.copy();
 
@@ -1213,7 +1216,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
       if (isTxCaching && cacheId != null && vs.getUrl() != null && cached.contains(vs.getUrl()+"|"+vs.getVersion())) {
         pin.addParameter().setName("url").setValue(new UriType(vs.getUrl()+(vs.hasVersion() ? "|"+vs.getVersion() : "")));        
       } else if (options.getVsAsUrl()){
-        pin.addParameter().setName("url").setValue(new StringType(vs.getUrl()));
+        pin.addParameter().setName("url").setValue(new UriType(vs.getUrl()));
       } else {
         pin.addParameter().setName("valueSet").setResource(vs);
         if (vs.getUrl() != null) {

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

@@ -77,6 +77,7 @@ import org.hl7.fhir.utilities.TimeTracker;
 import org.hl7.fhir.utilities.TranslationServices;
 import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationOptions;
@@ -338,6 +339,23 @@ public interface IWorkerContext {
      * @return
      */
     String patchUrl(String url, String resourceType);
+    
+    /** 
+     * set this to false (default is true) if you don't want profiles loaded
+     * @param value
+     * @return
+     */
+    IContextResourceLoader setLoadProfiles(boolean value);
+    
+    /**
+     * Called during the loading process - the loader can decide which resources to load. 
+     * At this point, only the .index.json is being read 
+     *  
+     * @param pi
+     * @param pri
+     * @return
+     */
+    boolean wantLoad(NpmPackage pi, PackageResourceInformation pri);
   }
 
   /**

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

@@ -492,7 +492,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
         types = Utilities.strings("StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem", "Measures" );
       }
       for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
-        if (!pri.getFilename().contains("ig-r4")) {
+        if (!pri.getFilename().contains("ig-r4") && (loader == null || loader.wantLoad(pi, pri))) {
           try {
             registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageInformation(pi));
             t++;

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

@@ -394,7 +394,7 @@ public class FmlParser extends ParserBase {
         if (rule.getChildrenByName("source").size() != 1 || !rule.getChildrenByName("source").get(0).hasChild("element"))
           throw lexer.error("Complex rules must have an explicit name");
         if (rule.getChildrenByName("source").get(0).hasChild("type"))
-          rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + rule.getChildrenByName("source").get(0).getNamedChildValue("type"));
+          rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + Utilities.capitalize(rule.getChildrenByName("source").get(0).getNamedChildValue("type")));
         else
           rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element"));
       }

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

@@ -1245,6 +1245,20 @@ public class StructureDefinition extends CanonicalResource {
     return null;
   }
 
+
+  public ElementDefinition getElementById(String id) {
+    if (id == null) {
+      return null;
+    }
+    for (ElementDefinition ed : getElement()) {
+      if (id.equals(ed.getId())) {
+        return ed;
+      }
+    }
+    return null;
+  }
+
+  
 // end addition
   }
 

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

@@ -72,7 +72,11 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
     TableModel model = gen.new TableModel("qtree="+q.getId(), context.getRules() == GenerationRules.IG_PUBLISHER);    
     model.setAlternating(true);
-    model.setDocoImg(context.getLink(KnownLinkType.SPEC) +"help16.png");
+    if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
+      model.setDocoImg(HierarchicalTableGenerator.help16AsData());    
+    } else {
+      model.setDocoImg(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "help16.png"));
+    }
     model.setDocoRef(context.getLink(KnownLinkType.SPEC)+"formats.html#table");
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Text"), translate("sd.hint", "Text for the item"), null, 0));
@@ -446,7 +450,11 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
     TableModel model = gen.new TableModel("qtree="+q.getId(), true);    
     model.setAlternating(true);
-    model.setDocoImg(context.getLink(KnownLinkType.SPEC) +"help16.png");
+    if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
+      model.setDocoImg(HierarchicalTableGenerator.help16AsData());    
+    } else {
+      model.setDocoImg(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "help16.png"));
+    }
     model.setDocoRef(context.getLink(KnownLinkType.SPEC)+"formats.html#table");
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Description & Constraints"), translate("sd.hint", "Additional information about the item"), null, 0));

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

@@ -15,6 +15,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.renderers.utils.BaseWrappers.BaseWrapper;
 import org.hl7.fhir.r5.renderers.utils.BaseWrappers.ResourceWrapper;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
+import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.KnownLinkType;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
@@ -63,7 +64,11 @@ public class QuestionnaireResponseRenderer extends ResourceRenderer {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
     TableModel model = gen.new TableModel("qtree="+qr.getId(), false);    
     model.setAlternating(true);
-    model.setDocoImg(context.getLink(KnownLinkType.SPEC) +"help16.png");
+    if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
+      model.setDocoImg(HierarchicalTableGenerator.help16AsData());   
+    } else {
+      model.setDocoImg(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "help16.png"));
+    }
     model.setDocoRef(context.getLink(KnownLinkType.SPEC)+"formats.html#table");
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Text"), translate("sd.hint", "Text for the item"), null, 0));
@@ -86,7 +91,11 @@ public class QuestionnaireResponseRenderer extends ResourceRenderer {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
     TableModel model = gen.new TableModel("qtree="+q.getId(), true);    
     model.setAlternating(true);
-    model.setDocoImg(context.getLink(KnownLinkType.SPEC) +"help16.png");
+    if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
+      model.setDocoImg(HierarchicalTableGenerator.help16AsData());      
+    } else {
+      model.setDocoImg(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "help16.png"));
+    }
     model.setDocoRef(context.getLink(KnownLinkType.SPEC)+"formats.html#table");
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Text"), translate("sd.hint", "Text for the item"), null, 0));

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

@@ -3,10 +3,12 @@ package org.hl7.fhir.r5.renderers;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
+import org.hl7.fhir.r5.renderers.utils.RenderingContext.KnownLinkType;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
 import org.hl7.fhir.r5.utils.TranslatingUtilities;
 import org.hl7.fhir.utilities.MarkDownProcessor;
 import org.hl7.fhir.utilities.StandardsStatus;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
 import org.hl7.fhir.utilities.validation.ValidationOptions;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@@ -76,7 +78,7 @@ public class Renderer extends TranslatingUtilities {
   public void genStandardsStatus(XhtmlNode td, StandardsStatus ss) {
     if (ss != null) {
       td.tx(" ");
-      XhtmlNode a = td.ah("versions.html#std-process", "Standards Status = "+ss.toDisplay());
+      XhtmlNode a = td.ah(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "versions.html#std-process"), "Standards Status = "+ss.toDisplay());
       a.style("padding-left: 3px; padding-right: 3px; border: 1px grey solid; font-weight: bold; color: black; background-color: "+ss.getColor());
       a.tx(ss.getAbbrev());
     }

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

@@ -516,11 +516,15 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
     }
   }
 
-  public TableModel initCustomTable(HierarchicalTableGenerator gen, String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, List<Column> columns) {
+  public TableModel initCustomTable(HierarchicalTableGenerator gen, String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, List<Column> columns) throws IOException {
     TableModel model = gen.new TableModel(id, isActive);
     
     model.setAlternating(alternating);
-    model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
+    if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
+      model.setDocoImg(HierarchicalTableGenerator.help16AsData());       
+    } else {
+      model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
+    }
     model.setDocoRef(Utilities.pathURL("https://build.fhir.org/ig/FHIR/ig-guidance", "readingIgs.html#table-views"));
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
     for (Column col : columns) {
@@ -2586,10 +2590,14 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
   }
 
 
-  private TableModel initSpanningTable(HierarchicalTableGenerator gen, String prefix, boolean isLogical, String id) {
+  private TableModel initSpanningTable(HierarchicalTableGenerator gen, String prefix, boolean isLogical, String id) throws IOException {
     TableModel model = gen.new TableModel(id, true);
     
-    model.setDocoImg(prefix+"help16.png");
+    if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
+      model.setDocoImg(HierarchicalTableGenerator.help16AsData());     
+    } else {
+      model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
+    }
     model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table")); // todo: change to graph definition
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Property", "A profiled resource", null, 0));
     model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Card.", "Minimum and Maximum # of times the the element can appear in the instance", null, 0));

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

@@ -461,7 +461,7 @@ public class StructureMapRenderer extends TerminologyRenderer {
     if (n.equals(s) || n.equals("\"" + s + "\""))
       return true;
     if (source.get(0).hasType()) {
-      s = source.get(0).getElement() + "-" + source.get(0).getType();
+      s = source.get(0).getElement() + Utilities.capitalize(source.get(0).getType());
       return n.equals(s) || n.equals("\"" + s + "\"");
     }
     return false;

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestPackageLoader.java

@@ -13,6 +13,7 @@ import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
 
 public class TestPackageLoader implements IContextResourceLoader {
 
@@ -62,4 +63,14 @@ public class TestPackageLoader implements IContextResourceLoader {
     return url;
   }
 
+  @Override
+  public IContextResourceLoader setLoadProfiles(boolean value) {
+    return this;
+  }
+
+  @Override
+  public boolean wantLoad(NpmPackage pi, PackageResourceInformation pri) {
+    return true;
+  }
+
 }

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

@@ -1000,7 +1000,7 @@ public class StructureMapUtilities {
         if (rule.getSource().size() != 1 || !rule.getSourceFirstRep().hasElement() && exceptionsForChecks )
           throw lexer.error("Complex rules must have an explicit name");
         if (rule.getSourceFirstRep().hasType())
-          rule.setName(rule.getSourceFirstRep().getElement() + "-" + rule.getSourceFirstRep().getType());
+          rule.setName(rule.getSourceFirstRep().getElement() + Utilities.capitalize(rule.getSourceFirstRep().getType()));
         else
           rule.setName(rule.getSourceFirstRep().getElement());
       }

org.hl7.fhir.report/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.113-SNAPSHOT</version>
+        <version>5.6.115-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>5.6.113-SNAPSHOT</version>
+        <version>5.6.115-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

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

@@ -115,15 +115,28 @@ public class FTPClient {
 
     resetTimers();
 
-    logger.debug("Initial Working directory: " + clientImpl.printWorkingDirectory());
+    clientImpl.setFileType(FTP.BINARY_FILE_TYPE);
+    clientImpl.enterLocalPassiveMode();
+
+    logger.debug("Setting initial working directory: " + clientImpl.printWorkingDirectory());
 
     clientImpl.changeWorkingDirectory(path);
 
     throwExceptionForNegativeCompletion("FTP server could not establish default working directory", true);
+    logger.debug("Set initial working directory.");
 
+    logger.debug("Resolving remote resolved path.");
     resolvedPath = clientImpl.printWorkingDirectory();
 
-    logger.debug("Resolved working directory: " + resolvedPath);
+    logger.debug("Resolved remote resolved path: " + resolvedPath);
+  }
+
+  public void setBufferSize(int bufferSize) {
+    clientImpl.setBufferSize(bufferSize);
+  }
+
+  public int getBufferSize() {
+    return clientImpl.getBufferSize();
   }
 
   private void resetTimers() {
@@ -208,7 +221,6 @@ public class FTPClient {
     String resolvedPath = resolveRemotePath(path);
     logger.debug("Uploading file to remote path: " + resolvedPath);
 
-
     attemptUpload(source, resolvedPath);
 
     FTPReplyCodeAndString reply = getFTPReplyCodeAndString();
@@ -239,8 +251,6 @@ public class FTPClient {
   private void attemptUpload(String source, String resolvedPath) throws IOException {
     final long startTime = System.nanoTime();
     FileInputStream localStream = new FileInputStream(source);
-    clientImpl.setFileType(FTP.BINARY_FILE_TYPE);
-    clientImpl.enterLocalPassiveMode();
     clientImpl.storeFile(resolvedPath, localStream);
     localStream.close();
     this.storeFileTimeNanos += System.nanoTime() - startTime;

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

@@ -905,6 +905,15 @@ public class Utilities {
     return false;
   }
 
+  public static boolean containsInList(String value, String... array) {
+    if (value == null)
+      return false;
+    for (String s : array)
+      if (value.contains(s))
+        return true;
+    return false;
+  }
+
   public static boolean existsInList(String value, String... array) {
     if (value == null)
       return false;
@@ -1491,10 +1500,13 @@ public class Utilities {
       ZipEntry zipEntry = zis.getNextEntry();
       while (zipEntry != null) {
         boolean isDirectory = false;
-        if (zipEntry.getName().endsWith("/") || zipEntry.getName().endsWith("\\")) {
+        
+        String n = makeOSSafe(zipEntry.getName());
+      
+        if (n.endsWith(File.separator)) {
           isDirectory = true;
         }
-        Path newPath = zipSlipProtect(zipEntry, target);
+        Path newPath = zipSlipProtect(n, target);
         if (isDirectory) {
           Files.createDirectories(newPath);
         } else {
@@ -1511,19 +1523,23 @@ public class Utilities {
     }
   }
 
-  public static Path zipSlipProtect(ZipEntry zipEntry, Path targetDir)
+  public static String makeOSSafe(String name) {
+    return name.replace("\\", File.separator).replace("/", File.separator);
+  }
+
+  public static Path zipSlipProtect(String zipName, Path targetDir)
       throws IOException {
 
     // test zip slip vulnerability
     // Path targetDirResolved = targetDir.resolve("../../" + zipEntry.getName());
 
-    Path targetDirResolved = targetDir.resolve(zipEntry.getName());
+    Path targetDirResolved = targetDir.resolve(zipName);
 
     // make sure normalized file still has targetDir as its prefix
     // else throws exception
     Path normalizePath = targetDirResolved.normalize();
     if (!normalizePath.startsWith(targetDir)) {
-      throw new IOException("Bad zip entry: " + zipEntry.getName());
+      throw new IOException("Bad zip entry: " + zipName);
     }
 
     return normalizePath;
@@ -1868,7 +1884,7 @@ public class Utilities {
       if (ignoreList == null || !ignoreList.contains(f.getAbsolutePath())) {
         if (f.isDirectory()) {
           addAllFiles(res, root, f, ignoreList);
-        } else {
+        } else if (!f.getName().equals(".DS_Store")) {
           res.add(getRelativePath(root, f.getAbsolutePath()));
         }
       }
@@ -1932,7 +1948,7 @@ public class Utilities {
 
   public static String tail(String url) {
     int i = url.length()-1;
-    while (i >= 0 && isTokenChar(url.charAt(i))) {
+    while (i >= 0 && (isTokenChar(url.charAt(i)) || isDigit(url.charAt(i))) ) {
       i--;
     }
     if (i < 0) {

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

@@ -668,6 +668,8 @@ public class I18nConstants {
   public static final String MEASURE_SHAREABLE_MISSING_HL7 = "MEASURE_SHAREABLE_MISSING_HL7";
   public static final String MEASURE_SHAREABLE_EXTRA_MISSING_HL7 = "MEASURE_SHAREABLE_EXTRA_MISSING_HL7";
   public static final String MEASURE_SHAREABLE_EXTRA_MISSING = "MEASURE_SHAREABLE_EXTRA_MISSING";
+  public static final String VALUESET_EXAMPLE_SYSTEM_ERROR = "VALUESET_EXAMPLE_SYSTEM_ERROR";
+  public static final String VALUESET_EXAMPLE_SYSTEM_HINT = "VALUESET_EXAMPLE_SYSTEM_HINT";
   public static final String VALUESET_UNC_SYSTEM_WARNING = "VALUESET_UNC_SYSTEM_WARNING";
   public static final String VALUESET_UNC_SYSTEM_WARNING_VER = "VALUESET_UNC_SYSTEM_WARNING_VER";
   public static final String VALUESET_IMPORT_UNION_INTERSECTION = "VALUESET_IMPORT_UNION_INTERSECTION";

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java

@@ -66,6 +66,7 @@ import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -82,9 +83,9 @@ import org.commonmark.node.Node;
 import org.commonmark.parser.Parser;
 import org.commonmark.renderer.html.HtmlRenderer;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.TranslatingUtilities;
 import org.hl7.fhir.utilities.Utilities;
-import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 
 
 public class HierarchicalTableGenerator extends TranslatingUtilities {
@@ -634,13 +635,17 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
     checkSetup();
   }
 
-  public TableModel initNormalTable(String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, TableGenerationMode mode) {
+  public TableModel initNormalTable(String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, TableGenerationMode mode) throws IOException {
     this.mode = mode;
     
     TableModel model = new TableModel(id, isActive);
     
     model.setAlternating(alternating);
-    model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
+    if (mode == TableGenerationMode.XML) {
+      model.setDocoImg(help16AsData());     
+    } else {
+      model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
+    }
     model.setDocoRef(Utilities.pathURL("https://build.fhir.org/ig/FHIR/ig-guidance", "readingIgs.html#table-views"));
     model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
     model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Flags"), translate("sd.hint", "Information about the use of the element"), null, 0));
@@ -653,11 +658,15 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
     return model;
   }
 
-  public TableModel initComparisonTable(String prefix, String id) {
+  public TableModel initComparisonTable(String prefix, String id) throws IOException {
     TableModel model = new TableModel(id, true);
     
     model.setAlternating(true);
-    model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
+    if (mode == TableGenerationMode.XML) {
+      model.setDocoImg(help16AsData()); // #FIXME      
+    } else {
+      model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
+    }
     model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table"));    
     model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
     model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "L Flags"), translate("sd.hint", "Information about the use of the element - Left Structure"), null, 0).setStyle("border-left: 1px grey solid"));
@@ -913,6 +922,15 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
       return corePrefix+filename;
   }
 
+  public static String help16AsData() throws IOException {
+    ClassLoader classLoader = HierarchicalTableGenerator.class.getClassLoader();
+    InputStream help = classLoader.getResourceAsStream("help16.png");
+    StringBuilder b = new StringBuilder();
+    b.append("data:image/png;base64,");
+    byte[] bytes = TextFile.streamToBytes(help);
+    b.append(new String(Base64.encodeBase64(bytes)));
+    return b.toString();
+  }
   
   private void checkModel(TableModel model) throws FHIRException  {
     check(!model.getTitles().isEmpty(), "Must have titles");

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XhtmlGenerator.java

@@ -187,7 +187,11 @@ public class XhtmlGenerator {
           out.write(" ");
         if (adorner != null) {
           XhtmlGeneratorAdornerState attrState = adorner.getAttributeMarkup(this, newstate, node, node.getAttributes().item(i).getNodeName(), node.getAttributes().item(i).getTextContent());
-          out.write(node.getAttributes().item(i).getNodeName()+"=\"<span class=\"xmlattrvalue\">"+attrState.getPrefix()+escapeHtml(Utilities.escapeXml(node.getAttributes().item(i).getTextContent()), level)+attrState.getSuffix()+"</span>\"");
+          if (attrState.getAltText() != null) {
+            out.write(node.getAttributes().item(i).getNodeName()+"=\"<span class=\"xmlattrvalue\">"+attrState.getPrefix()+escapeHtml(Utilities.escapeXml(attrState.getAltText()), level)+attrState.getSuffix()+"</span>\"");
+          } else {
+            out.write(node.getAttributes().item(i).getNodeName()+"=\"<span class=\"xmlattrvalue\">"+attrState.getPrefix()+escapeHtml(Utilities.escapeXml(node.getAttributes().item(i).getTextContent()), level)+attrState.getSuffix()+"</span>\"");
+          }
         } else
           out.write(node.getAttributes().item(i).getNodeName()+"=\"<span class=\"xmlattrvalue\">"+escapeHtml(Utilities.escapeXml(node.getAttributes().item(i).getTextContent()), level)+"</span>\"");
       }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XhtmlGeneratorAdorner.java

@@ -41,6 +41,7 @@ public interface XhtmlGeneratorAdorner {
     private String suffix;
     private String supressionMessage;
     private String path;
+    private String altText;
     
     public XhtmlGeneratorAdornerState(String path, String prefix, String suffix) {
       super();
@@ -49,6 +50,15 @@ public interface XhtmlGeneratorAdorner {
       this.suffix = suffix;
     }
     
+
+    public XhtmlGeneratorAdornerState(String path, String prefix, String suffix, String altText) {
+      super();
+      this.path = path;
+      this.prefix = prefix;
+      this.suffix = suffix;
+      this.altText = altText;
+    }
+    
     public XhtmlGeneratorAdornerState(String path, String supressionMessage) {
       super();
       this.path = path;
@@ -70,6 +80,11 @@ public interface XhtmlGeneratorAdorner {
     public String getPath() {
       return path;
     }
+
+    public String getAltText() {
+      return altText;
+    }
+
   }
   
   XhtmlGeneratorAdornerState getState(XhtmlGenerator ref, XhtmlGeneratorAdornerState state, Element node) throws Exception;

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

@@ -558,6 +558,8 @@ SEARCHPARAMETER_EXP_WRONG = The expression ''{2}'' is not compatible with the ex
 VALUESET_NO_SYSTEM_WARNING = No System specified, so Concepts and Filters can't be checked
 VALUESET_INCLUDE_INVALID_CONCEPT_CODE = The code {1} is not valid in the system {0}
 VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER = The code {2} is not valid in the system {0} version {1}
+VALUESET_EXAMPLE_SYSTEM_HINT = Example System ''{0}'' specified, so Concepts and Filters can''t be checked
+VALUESET_EXAMPLE_SYSTEM_ERROR = Example System ''{0}'' specified, which is illegal. Concepts and Filters can''t be checked
 VALUESET_UNC_SYSTEM_WARNING = Unknown System ''{0}'' specified, so Concepts and Filters can''t be checked (Details: {1})
 VALUESET_UNC_SYSTEM_WARNING_VER = Unknown System/Version ''{0}'' specified, so Concepts and Filters can''t be checked (Details: {1})
 Extension_PROF_Type = The Profile ''{0}'' definition allows for the type {1} but found type {2}
@@ -855,7 +857,7 @@ SM_NO_LIST_RULE_ID_NEEDED = A list ruleId should not be provided since this is a
 SM_LIST_RULE_ID_ONLY_WHEN_SHARE = A ruleId should only be provided when the rule mode is ''share''
 SM_RULE_SOURCE_UNASSIGNED = The source statement doesn''t assign a variable to the source - check that this is what is intended
 SM_TARGET_PATH_MULTIPLE_MATCHES = The target path {0}.{1} refers to the path {2} which is could be a reference to multiple elements ({3}). No further checking can be performed
-SM_SOURCE_TYPE_INVALID = The type {0} is not valid in this source context {1}. The possible types are [{2}]
+SM_SOURCE_TYPE_INVALID = The type {0} is not valid in the source context {1}. The possible types are [{2}]
 SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE = Transform {0} takes {1}-{2} parameter(s) but {3} were found
 SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE = Transform {0} takes {1} parameter(s) but {2} were found
 SM_TARGET_TRANSFORM_NOT_CHECKED = Transform {0} not checked  dyet

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/FTPClientTest.java

@@ -30,8 +30,11 @@ public class FTPClientTest implements ResourceLoaderTests {
   public static final String DUMMY_FILE_TO_DELETE = "dummyFileToDelete";
 
   public static final String DUMMY_FILE_TO_UPLOAD = "dummyFileToUpload";
+
+  public static final String DUMMY_FILE_TO_UPLOAD_2 = "dummyFileToUpload2";
   public static final int FAKE_FTP_PORT = 8022;
   public static final String DUMMY_FILE_CONTENT = "Dummy file content\nMore content\n";
+  public static final String DUMMY_FILE_CONTENT_2 = "Dummy file content 2\nMore content\n";
   public static final String LOCALHOST = "localhost";
 
 
@@ -48,26 +51,31 @@ public class FTPClientTest implements ResourceLoaderTests {
 
 
   Path dummyFileToUploadPath;
+
+  Path dummyFileToUploadPath2;
   Path dummyUploadedFilePath;
+  Path dummyUploadedFilePath2;
 
   String dummyFileContent;
 
+  String dummyFileContent2;
+
   @BeforeEach
   public void setup() throws IOException {
-    setupDummyFileToUpload();
+    setupDummyFilesToUpload();
     setupFakeFtpDirectory();
     setupFakeFtpServer();
   }
 
-  private void setupDummyFileToUpload() throws IOException {
+  private void setupDummyFilesToUpload() throws IOException {
-    dummyFileContent = createDummyFileContent();
+    dummyFileContent = DUMMY_FILE_CONTENT;
+    dummyFileContent2 = DUMMY_FILE_CONTENT;
 
     dummyFileToUploadPath = Files.createTempFile("dummyFtpFileToUpload", "dummy");
     Files.write(dummyFileToUploadPath, DUMMY_FILE_CONTENT.getBytes(StandardCharsets.UTF_8));
-  }
 
-  private String createDummyFileContent() {
+    dummyFileToUploadPath2 = Files.createTempFile("dummyFtpFileToUpload2", "dummy");
-    return DUMMY_FILE_CONTENT;
+    Files.write(dummyFileToUploadPath2, DUMMY_FILE_CONTENT_2.getBytes(StandardCharsets.UTF_8));
   }
 
   public void setupFakeFtpServer() throws IOException {
@@ -101,6 +109,7 @@ public class FTPClientTest implements ResourceLoaderTests {
 
     dummyFileToDeletePath = Files.createFile(relativePath2.resolve(DUMMY_FILE_TO_DELETE));
     dummyUploadedFilePath = relativePath2.resolve(DUMMY_FILE_TO_UPLOAD);
+    dummyUploadedFilePath2 = relativePath2.resolve(DUMMY_FILE_TO_UPLOAD_2);
   }
 
   @AfterEach
@@ -141,6 +150,7 @@ public class FTPClientTest implements ResourceLoaderTests {
 
   private  FTPClient connectToFTPClient() throws IOException {
     FTPClient client = new FTPClient(LOCALHOST, FAKE_FTP_PORT,  RELATIVE_PATH_1, DUMMY_USER, DUMMY_PASSWORD);
+    client.setBufferSize(16000);
     client.connect();
 
     assertAllMillisFieldsAreZero(client);
@@ -175,21 +185,43 @@ public class FTPClientTest implements ResourceLoaderTests {
 
     client.upload(dummyFileToUploadPath.toFile().getAbsolutePath(), RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_UPLOAD);
 
-    assertUploadedFileCorrect(uploadFilePath);
+    assertUploadedFileCorrect(uploadFilePath, DUMMY_FILE_CONTENT);
 
     assertTrue(client.getDeleteFileTimeNanos() == 0);
     assertTrue(client.getStoreFileTimeNanos() > 0);
     assertTrue(client.getCreateRemotePathIfNotExistsNanos() == 0);
   }
 
-  private void assertUploadedFileCorrect(String uploadedFilePath) throws IOException {
+  @Test
+  public void testMultiUpload() throws IOException  {
+    FTPClient client = connectToFTPClient();
+
+    String uploadFilePath = dummyUploadedFilePath.toFile().getAbsolutePath();
+    assertFalse(fakeFtpServer.getFileSystem().exists(uploadFilePath));
+
+    String uploadFilePath2 = dummyUploadedFilePath2.toFile().getAbsolutePath();
+    assertFalse(fakeFtpServer.getFileSystem().exists(uploadFilePath));
+
+    client.upload(dummyFileToUploadPath.toFile().getAbsolutePath(), RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_UPLOAD);
+
+    client.upload(dummyFileToUploadPath2.toFile().getAbsolutePath(), RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_UPLOAD_2);
+
+    assertUploadedFileCorrect(uploadFilePath, DUMMY_FILE_CONTENT);
+    assertUploadedFileCorrect(uploadFilePath2, DUMMY_FILE_CONTENT_2);
+
+    assertTrue(client.getDeleteFileTimeNanos() == 0);
+    assertTrue(client.getStoreFileTimeNanos() > 0);
+    assertTrue(client.getCreateRemotePathIfNotExistsNanos() == 0);
+  }
+
+  private void assertUploadedFileCorrect(String uploadedFilePath, String expectedFileContent) throws IOException {
     assertTrue(fakeFtpServer.getFileSystem().exists(uploadedFilePath));
     FileEntry fileEntry = (FileEntry)fakeFtpServer.getFileSystem().getEntry(uploadedFilePath);
     assertNotNull(fileEntry);
     InputStream inputStream = fileEntry.createInputStream();
     byte[] bytes = IOUtils.toByteArray(inputStream);
     String actualContent = new String(bytes, StandardCharsets.UTF_8);
-    assertEquals(DUMMY_FILE_CONTENT,actualContent);
+    assertEquals(expectedFileContent,actualContent);
   }
 
   @Test
@@ -237,7 +269,7 @@ public class FTPClientTest implements ResourceLoaderTests {
     assertTrue(fakeFtpServer.getFileSystem().exists(newPath1.toFile().getAbsolutePath()));
     assertTrue(fakeFtpServer.getFileSystem().exists(newPath2.toFile().getAbsolutePath()));
 
-    assertUploadedFileCorrect(uploadFilePath.toFile().getAbsolutePath());
+    assertUploadedFileCorrect(uploadFilePath.toFile().getAbsolutePath(), DUMMY_FILE_CONTENT);
 
     assertTrue(client.getDeleteFileTimeNanos() == 0);
     assertTrue(client.getStoreFileTimeNanos() > 0);

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>5.6.113-SNAPSHOT</version>
+        <version>5.6.115-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>5.6.113-SNAPSHOT</version>
+        <version>5.6.115-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

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

@@ -155,6 +155,7 @@ public class BaseValidator implements IValidationContextResourceLoader {
   protected List<ValidationMessage> messagesToRemove = new ArrayList<>();
   private ValidationLevel level = ValidationLevel.HINTS;
   protected Coding jurisdiction;
+  protected boolean allowExamples;
 
   public BaseValidator(IWorkerContext context, XVerExtensionManager xverManager) {
     super();
@@ -1231,4 +1232,17 @@ public class BaseValidator implements IValidationContextResourceLoader {
     String url = cr.getChildValue("url");
     return url != null && url.contains("hl7");
   }
+
+  public boolean isAllowExamples() {
+    return this.allowExamples;
+  }
+
+  public void setAllowExamples(boolean value) {
+    this.allowExamples = value;
+  }
+
+  protected boolean isExampleUrl(String url) {
+    return Utilities.containsInList(url, "example.org", "acme.com", "acme.org");
+    
+  }
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/codesystem/CodeSystemValidator.java

@@ -65,8 +65,10 @@ public class CodeSystemValidator extends BaseValidator {
 
   private void checkCodes(Set<String> codes, List<ConceptDefinitionComponent> list, String path, List<ValidationMessage> errors) {
     for (ConceptDefinitionComponent cc : list) {
-      String npath = path+".concept.descendents().where(code = '"+cc.getCode()+"')";
+      String npath = path+".concept.where(code = '"+cc.getCode()+"')";
-      rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, npath, !codes.contains(cc.getCode()), "Duplicate Code "+cc.getCode());
+      if (codes.contains(cc.getCode())) {
+        rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, npath, false, "Duplicate Code "+cc.getCode());
+      }
       codes.add(cc.getCode());
       checkCodes(codes, cc.getConcept(), npath, errors);
     }

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

@@ -471,7 +471,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   private IValidationProfileUsageTracker tracker;
   private ValidatorHostServices validatorServices;
   private boolean assumeValidRestReferences;
-  private boolean allowExamples;
   private boolean securityChecks;
   private ProfileUtilities profileUtilities;
   private boolean crumbTrails;
@@ -586,14 +585,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     this.assumeValidRestReferences = value;
   }
 
-  public boolean isAllowExamples() {
-    return this.allowExamples;
-  }
-
-  public void setAllowExamples(boolean value) {
-    this.allowExamples = value;
-  }
-
   public boolean isAllowComments() {
     return allowComments;
   }
@@ -2646,7 +2637,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     if (fetcher != null && !type.equals("uuid")) {
       boolean found;
       try {
-        found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com")) || url.contains("acme.org")) || (url.startsWith("http://hl7.org/fhir/tools")) || 
+        found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com")) || url.contains("acme.org")) /* || (url.startsWith("http://hl7.org/fhir/tools")) */ || 
             SpecialExtensions.isKnownExtension(url) || isXverUrl(url);
         if (!found) {
           found = fetcher.resolveURL(this, hostContext, path, url, type);
@@ -5043,7 +5034,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     } else if (element.getType().equals("StructureMap")) {
       return new StructureMapValidator(context, timeTracker, fpe, xverManager,profileUtilities, jurisdiction).validateStructureMap(errors, element, stack);
     } else if (element.getType().equals("ValueSet")) {
-      return new ValueSetValidator(context, timeTracker, this, xverManager, jurisdiction).validateValueSet(errors, element, stack);
+      return new ValueSetValidator(context, timeTracker, this, xverManager, jurisdiction, allowExamples).validateValueSet(errors, element, stack);
     } else {
       return true;
     }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureMapValidator.java

@@ -199,6 +199,11 @@ public class StructureMapValidator extends BaseValidator {
       return sd.getUrl().equals(other.sd.getUrl()) && ed.getPath().equals(other.ed.getPath()) && Utilities.stringsEqual(type, other.type);
     }
 
+    @Override
+    public String toString() {
+      return summary();
+    }
+
   }
 
   public class VariableSet {
@@ -623,9 +628,15 @@ public class StructureMapValidator extends BaseValidator {
           } else {
             ok = false;
           }
+          // check condition
+          // check check
+        }
+      } else {
+        String variable = source.getChildValue("variable");
+        if (variable != null) {
+          variables.add(variable, v.getMode()); // may overwrite
+
         }      
-        // check condition
-        // check check
       }
     } 
     return ok;
@@ -873,7 +884,7 @@ public class StructureMapValidator extends BaseValidator {
     // under some special conditions, we can infer what the type will be:
     //  * there's a nominated default variable 
     //  * that variable has as single type
-    //  * there's a create with no param
+    //  * there's a create/copy with no param
     //  * there's a single dependent rule with name = StructureMapUtilities.DEF_GROUP_NAME
     //  * there's a default type group for the type of the source type 
     // otherwise, we can't know the target type. 
@@ -882,11 +893,25 @@ public class StructureMapValidator extends BaseValidator {
       VariableDefn v = variables.getVariable(ruleInfo.getDefVariable(), SOURCE);
       if (v != null && v.getEd() != null  && (v.getEd().getType().size() == 1 || v.getType() != null)) {
         List<Element> dependents = rule.getChildrenByName("dependent");
+        String type = v.getType() != null ? getTypeFromDefn(v.getEd(), v.getType()) : v.getEd().getTypeFirstRep().getWorkingCode();
         if (dependents.size() == 1 && StructureMapUtilities.DEF_GROUP_NAME.equals(dependents.get(0).getChildValue("name"))) {
-          String type = v.getType() != null ? getTypeFromDefn(v.getEd(), v.getType()) : v.getEd().getTypeFirstRep().getWorkingCode();
           // now, we look for a default group.
           // todo: look in this source
           // now look through the inputs
+          for (StructureMap map : imports) {
+            for (StructureMapGroupComponent grp : map.getGroup()) {
+              if (grp.getTypeMode() != StructureMapGroupTypeMode.NULL && grp.getInput().size() == 2) {
+                String grpType = getTypeForGroupInput(map, grp, grp.getInput().get(0));
+                if (sameTypes(type, grpType)) {
+                  String tgtType = getTypeForGroupInput(map, grp, grp.getInput().get(1));
+                  if (tgtType != null) {
+                    return tgtType;
+                  }
+                }
+              }
+            }
+          }
+        } else if (dependents.size() == 0) {
           for (StructureMap map : imports) {
             for (StructureMapGroupComponent grp : map.getGroup()) {
               if (grp.getTypeMode() == StructureMapGroupTypeMode.TYPEANDTYPES && grp.getInput().size() == 2) {
@@ -900,6 +925,7 @@ public class StructureMapValidator extends BaseValidator {
               }
             }
           }
+          
         }
       }
     }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ValueSetValidator.java

@@ -43,13 +43,13 @@ public class ValueSetValidator extends BaseValidator {
 
   private InstanceValidator parent;
 
-  public ValueSetValidator(IWorkerContext context, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction) {
+  public ValueSetValidator(IWorkerContext context, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction, boolean allowExamples) {
     super(context, xverManager);
     source = Source.InstanceValidator;
     this.timeTracker = timeTracker;
     this.parent = parent;
     this.jurisdiction = jurisdiction;
-
+    this.allowExamples = allowExamples;
   }
   
   public boolean validateValueSet(List<ValidationMessage> errors, Element vs, NodeStack stack) {
@@ -190,7 +190,15 @@ public class ValueSetValidator extends BaseValidator {
     if (version == null) {
       ValidationResult vv = context.validateCode(ValidationOptions.defaults(), new Coding(system, code, null), null);
       if (vv.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
-        warning(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stackInc.getLiteralPath(), false, I18nConstants.VALUESET_UNC_SYSTEM_WARNING, system, vv.getMessage());                      
+        if (isExampleUrl(system)) {
+          if (isAllowExamples()) {
+            hint(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stackInc.getLiteralPath(), false, I18nConstants.VALUESET_EXAMPLE_SYSTEM_HINT, system);
+          } else {
+            rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stackInc.getLiteralPath(), false, I18nConstants.VALUESET_EXAMPLE_SYSTEM_ERROR, system);
+          }
+        } else {
+          warning(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stackInc.getLiteralPath(), false, I18nConstants.VALUESET_UNC_SYSTEM_WARNING, system, vv.getMessage());
+        }
         return false;
       } else {
         boolean ok = vv.isOk();

pom.xml

@@ -14,12 +14,12 @@
     HAPI FHIR
     -->
     <artifactId>org.hl7.fhir.core</artifactId>
-    <version>5.6.113-SNAPSHOT</version>
+    <version>5.6.115-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <properties>
         <hapi_fhir_version>6.2.1</hapi_fhir_version>
-        <validator_test_case_version>1.2.21</validator_test_case_version>
+        <validator_test_case_version>1.2.23</validator_test_case_version>
         <junit_jupiter_version>5.7.1</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
         <maven_surefire_version>3.0.0-M5</maven_surefire_version>