Gg v5118 (#368)

* fix issue validating # references

* Mark it has an error if a JSON Array is empty

* Don't make wrong error reports for profiling resources in bundles

* * Render binding description in profile tables if it doesn't contain paragraphs
* fix bug with wrong value for contentReference in derived profiles (profiles do not and cannot change the value)

* fix bug with wrong value for contentReference in derived profiles (profiles do not and cannot change the value) (missed testing change)

* * fix bug not recognising some content as xml or json

* improved markdown support in table generator

* * fix bug checking unfixed values for HumanName patterns
* fix bug checking patterns (missed in some circumstances)
* fix bug checking type of resources in bundles
* improve messages around cardinality errors in profiles

* add parameter -html-output for enhanced presentation of slicing information (issue #283)

RELEASE_NOTES.md

@@ -0,0 +1,12 @@
+Validator Changes:
+* Mark it has an error if a JSON Array is empty 
+* Don't make wrong error reports for profiling resources in bundles
+* fix bug checking unfixed values for HumanName patterns
+* fix bug checking patterns (missed in some circumstances)
+* fix bug checking type of resources in bundles
+* improve messages around cardinality errors in profiles
+* add parameter -html-output for enhanced presentation of slicing information
+
+Other code changes:
+* Render binding description in profile tables if it doesn't contain paragraphs
+* fix bug with wrong value for contentReference in derived profiles (profiles do not and cannot change the value)

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

@@ -111,6 +111,7 @@ import org.hl7.fhir.r5.utils.XVerExtensionManager.XVerExtensionStatus;
 import org.hl7.fhir.r5.utils.formats.CSVWriter;
 import org.hl7.fhir.r5.utils.formats.XLSXWriter;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.MarkDownProcessor;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
@@ -362,9 +363,28 @@ public class ProfileUtilities extends TranslatingUtilities {
 
 
   public List<ElementDefinition> getChildMap(StructureDefinition profile, ElementDefinition element) throws DefinitionException {
-    if (element.getContentReference()!=null) {
+    if (element.getContentReference() != null) {
-      for (ElementDefinition e : profile.getSnapshot().getElement()) {
+      List<ElementDefinition> list = null;
-        if (element.getContentReference().equals("#"+e.getId()))
+      String id = null;
+      if (element.getContentReference().startsWith("#")) {
+        // internal reference
+        id = element.getContentReference().substring(1);
+        list = profile.getSnapshot().getElement();
+      } else if (element.getContentReference().contains("#")) {
+        // external reference
+        String ref = element.getContentReference();
+        StructureDefinition sd = context.fetchResource(StructureDefinition.class, ref.substring(0, ref.indexOf("#")));
+        if (sd == null) {
+          throw new DefinitionException("unable to process contentReference '"+element.getContentReference()+"' on element '"+element.getId()+"'");
+        }
+        list = sd.getSnapshot().getElement();
+        id = ref.substring(ref.indexOf("#")+1);        
+      } else {
+        throw new DefinitionException("unable to process contentReference '"+element.getContentReference()+"' on element '"+element.getId()+"'");
+      }
+        
+      for (ElementDefinition e : list) {
+        if (id.equals(e.getId()))
           return getChildMap(profile, e);
       }
       throw new DefinitionException(context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_NAME_REFERENCE__AT_PATH_, element.getContentReference(), element.getPath()));
@@ -3155,6 +3175,10 @@ public class ProfileUtilities extends TranslatingUtilities {
         c.getPieces().add(checkForNoChange(ved.getBinding(), gen.new Piece(corePath+"terminologies.html#"+ved.getBinding().getStrength().toCode(), egt(ved.getBinding().getStrengthElement()), ved.getBinding().getStrength().getDefinition())));              
         c.getPieces().add(gen.new Piece(null, ")", null));
       }
+      if (ved.getBinding().hasDescription() && MarkDownProcessor.isSimpleMarkdown(ved.getBinding().getDescription())) {
+        c.getPieces().add(gen.new Piece(null, ": ", null));
+        c.addMarkdownNoPara(ved.getBinding().getDescription());
+      }
     }
     c.addPiece(gen.new Piece("br")).addPiece(gen.new Piece(null, describeExtensionContext(ed), null));
     r.getCells().add(c);
@@ -4282,6 +4306,10 @@ public class ProfileUtilities extends TranslatingUtilities {
               c.getPieces().add(checkForNoChange(binding, gen.new Piece(corePath+"extension-elementdefinition-minvalueset.html", translate("sd.table", "Min Binding")+": ", "Min Value Set Extension").addStyle("font-weight:bold")));             
               c.getPieces().add(checkForNoChange(binding, gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath+br.url, br.display, null)));
             }
+            if (binding.hasDescription() && MarkDownProcessor.isSimpleMarkdown(binding.getDescription())) {
+              c.getPieces().add(gen.new Piece(null, ": ", null));
+              c.addMarkdownNoPara(binding.getDescription());
+            }
           }
           for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {
             if (!inv.hasSource() || profile == null || inv.getSource().equals(profile.getUrl()) || allInvariants) {
@@ -4300,7 +4328,6 @@ public class ProfileUtilities extends TranslatingUtilities {
               // don't show this, this it's important: c.getPieces().add(gen.new Piece(null, "This repeating element has no defined order", null));
             }           
           }
-
           if (definition.hasFixed()) {
             if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
             c.getPieces().add(checkForNoChange(definition.getFixed(), gen.new Piece(null, translate("sd.table", "Fixed Value")+": ", null).addStyle("font-weight:bold")));
@@ -4594,6 +4621,10 @@ public class ProfileUtilities extends TranslatingUtilities {
               c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, " (", null)));
               c.getPieces().add(checkForNoChange(binding, gen.new Piece(corePath+"terminologies.html#"+binding.getStrength().toCode(), binding.getStrength().toCode(), binding.getStrength().getDefinition())));              c.getPieces().add(gen.new Piece(null, ")", null));
             }
+            if (binding.hasDescription() && MarkDownProcessor.isSimpleMarkdown(binding.getDescription())) {
+              c.getPieces().add(gen.new Piece(null, ": ", null));
+              c.addMarkdownNoPara(binding.getDescription());
+            }
           }
           for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {
             if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
@@ -5338,12 +5369,12 @@ public class ProfileUtilities extends TranslatingUtilities {
     if (!checkFirst || !sd.hasDifferential() || hasMissingIds(sd.getDifferential().getElement())) {
       if (!sd.hasDifferential())
         sd.setDifferential(new StructureDefinitionDifferentialComponent());
-      generateIds(sd.getDifferential().getElement(), sd.getUrl());
+      generateIds(sd.getDifferential().getElement(), sd.getUrl(), sd.getType());
     }
     if (!checkFirst || !sd.hasSnapshot() || hasMissingIds(sd.getSnapshot().getElement())) {
       if (!sd.hasSnapshot())
         sd.setSnapshot(new StructureDefinitionSnapshotComponent());
-      generateIds(sd.getSnapshot().getElement(), sd.getUrl());
+      generateIds(sd.getSnapshot().getElement(), sd.getUrl(), sd.getType());
     }
   }
 
@@ -5388,11 +5419,10 @@ public class ProfileUtilities extends TranslatingUtilities {
 
   }
 
-  private void generateIds(List<ElementDefinition> list, String name) throws DefinitionException  {
+  private void generateIds(List<ElementDefinition> list, String name, String type) throws DefinitionException  {
     if (list.isEmpty())
       return;
     
-    Map<String, String> idMap = new HashMap<String, String>();
     Map<String, String> idList = new HashMap<String, String>();
     
     SliceList sliceInfo = new SliceList();
@@ -5420,7 +5450,6 @@ public class ProfileUtilities extends TranslatingUtilities {
         }
       }
       String bs = b.toString();
-      idMap.put(ed.hasId() ? ed.getId() : ed.getPath(), bs);
       ed.setId(bs);
       if (idList.containsKey(bs)) {
         if (exception || messages == null) {
@@ -5429,11 +5458,9 @@ public class ProfileUtilities extends TranslatingUtilities {
           messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, name+"."+bs, "Duplicate Element id "+bs, ValidationMessage.IssueSeverity.ERROR));
       }
       idList.put(bs, ed.getPath());
-      if (ed.hasContentReference()) {
+      if (ed.hasContentReference() && ed.getContentReference().startsWith("#")) {
-        String s = ed.getContentReference().substring(1);
+        String s = ed.getContentReference();
-        if (idMap.containsKey(s))
+        ed.setContentReference("http://hl7.org/fhir/StructureDefinition/"+type+s);
-          ed.setContentReference("#"+idMap.get(s));
-        
       }
     }  
     // second path - fix up any broken path based id references

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

@@ -208,6 +208,9 @@ public class JsonParser extends ParserBase {
 		JsonElement e = object.get(name);
 		if (property.isList() && (e instanceof JsonArray)) {
 			JsonArray arr = (JsonArray) e;
+			if (arr.size() == 0) {
+        logError(line(e), col(e), npath, IssueType.INVALID, context.formatMessage(I18nConstants.ARRAY_CANNOT_BE_EMPTY), IssueSeverity.ERROR);			  
+			}
 			int c = 0;
 			for (JsonElement am : arr) {
 				parseChildComplexInstance(npath+"["+c+"]", object, element, property, name, am);

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

@@ -46,6 +46,7 @@ public class OperationOutcomeUtilities {
 
   public static OperationOutcomeIssueComponent convertToIssue(ValidationMessage message, OperationOutcome op) {
     OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
+    issue.setUserData("source.vm", message);   
     issue.setCode(convert(message.getType()));
     
     if (message.getLocation() != null) {

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ProfileUtilitiesTests.java

@@ -104,6 +104,8 @@ public class ProfileUtilitiesTests {
           f.setComment(null);
           b.setDefinition(null);
           f.setDefinition(null);
+          b.setContentReference(null);
+          f.setContentReference(null);
           ok = Base.compareDeep(b, f, true);
         }
       }

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

@@ -79,4 +79,9 @@ public class MarkDownProcessor {
     return html;  
   }
 
+
+  public static boolean isSimpleMarkdown(String description) {
+    return !description.contains("\n");
+  }
+  
 }

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

@@ -12,6 +12,7 @@ public class I18nConstants {
   public static final String ALL_OBSERVATIONS_SHOULD_HAVE_A_PERFORMER = "All_observations_should_have_a_performer";
   public static final String ALL_OBSERVATIONS_SHOULD_HAVE_A_SUBJECT = "All_observations_should_have_a_subject";
   public static final String ALL_OK = "ALL_OK";
+  public static final String ARRAY_CANNOT_BE_EMPTY = "ARRAY_CANNOT_BE_EMPTY";
   public static final String ATTEMPT_TO_A_SLICE_AN_ELEMENT_THAT_DOES_NOT_REPEAT__FROM__IN_ = "Attempt_to_a_slice_an_element_that_does_not_repeat__from__in_";
   public static final String ATTEMPT_TO_REPLACE_ELEMENT_NAME_FOR_A_NONCHOICE_TYPE = "Attempt_to_replace_element_name_for_a_nonchoice_type";
   public static final String ATTEMPT_TO_USE_A_SNAPSHOT_ON_PROFILE__AS__BEFORE_IT_IS_GENERATED = "Attempt_to_use_a_snapshot_on_profile__as__before_it_is_generated";

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

@@ -240,6 +240,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
       pieces.add(piece);
       return this;
     }
+    
     public Cell addMarkdown(String md) {
       try {
         Parser parser = Parser.builder().build();
@@ -253,6 +254,19 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
       return this;
     }
     
+    public Cell addMarkdownNoPara(String md) {
+      try {
+        Parser parser = Parser.builder().build();
+        Node document = parser.parse(md);
+        HtmlRenderer renderer = HtmlRenderer.builder().escapeHtml(true).build();
+        String html = renderer.render(document);  
+        pieces.addAll(htmlToParagraphPieces(html));
+      } catch (Exception e) {
+        e.printStackTrace();
+      }
+      return this;
+    }
+    
     private List<Piece> htmlToParagraphPieces(String html)  {
       List<Piece> myPieces = new ArrayList<Piece>();
       try {

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

@@ -209,11 +209,12 @@ Validation_BUNDLE_Message = The first entry in a message must be a MessageHeader
 Validation_VAL_Content_Unknown = Unrecognised Content {0}
 Validation_VAL_NoType = Unknown type {0}
 Validation_VAL_Profile_MatchMultiple = Profile {0}, Element matches more than one slice - {1}, {2}
-Validation_VAL_Profile_Maximum = {0}: max allowed = {1}, but found {2}
+// for the next 4 messages, the available parameters are: 0: profile url, 1: ed.path, 2: ed.id, 3: ed.sliceName, 4: ed.label, 5: element.path, 6: ed.min and optionally 7: actual count
-Validation_VAL_Profile_Minimum = {0}: minimum required = {1}, but only found {2}
+Validation_VAL_Profile_Maximum = {2}: max allowed = {6}, but found {7} (from {0})
+Validation_VAL_Profile_Minimum = {2}: minimum required = {6}, but only found {7} (from {0})
+Validation_VAL_Profile_NoCheckMax = {2}: Unable to check max allowed ({1}) due to lack of slicing validation (from {0})
+Validation_VAL_Profile_NoCheckMin = {2}: Unable to check minimum required ({1}) due to lack of slicing validation (from {0})
 Validation_VAL_Profile_MultipleMatches = Found multiple matching profiles among choices: {0}
-Validation_VAL_Profile_NoCheckMax = {0}: Unable to check max allowed ({1}) due to lack of slicing validation
-Validation_VAL_Profile_NoCheckMin = {0}'': Unable to check minimum required ({1}) due to lack of slicing validation
 Validation_VAL_Profile_NoDefinition = No definition found for resource type ''{0}''
 Validation_VAL_Profile_NoMatch = Unable to find matching profile among choices: {0}
 Validation_VAL_Profile_NoSnapshot = StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided
@@ -617,4 +618,5 @@ SD_ED_TYPE_PROFILE_NOTYPE = Found profile {0}, but unable to determine the type
 SD_ED_TYPE_PROFILE_WRONG = Profile {0} is for type {1}, but this element has type {2} 
 TERMINOLOGY_TX_NOSVC_BOUND_REQ = Could not confirm that the codes provided are from the required value set {0} because there is no terminology service
 TERMINOLOGY_TX_NOSVC_BOUND_EXT = Could not confirm that the codes provided are from the extensible value set {0} because there is no terminology service
+ARRAY_CANNOT_BE_EMPTY = Array cannot be empty - the property should not be present if it has no values
         

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

@@ -29,6 +29,10 @@ import java.util.UUID;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
 import org.hl7.fhir.convertors.VersionConvertor_10_30;
@@ -56,6 +60,7 @@ import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
+import org.hl7.fhir.r5.elementmodel.ParserBase.ValidationPolicy;
 import org.hl7.fhir.r5.elementmodel.ObjectConverter;
 import org.hl7.fhir.r5.formats.FormatUtilities;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
@@ -98,19 +103,23 @@ import org.hl7.fhir.utilities.TimeTracker;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
+import org.hl7.fhir.utilities.json.JsonTrackingParser;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.npm.ToolsVersion;
+import org.hl7.fhir.utilities.turtle.Turtle;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
 import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 import org.hl7.fhir.validation.BaseValidator.ValidationControl;
+import org.hl7.fhir.validation.ValidationEngine.ValidationRecord;
 import org.hl7.fhir.validation.cli.model.ScanOutputItem;
 import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
 import org.hl7.fhir.validation.cli.utils.*;
 import org.hl7.fhir.validation.instance.InstanceValidator;
+import org.w3c.dom.Document;
 import org.xml.sax.SAXException;
 
 
@@ -187,6 +196,50 @@ POSSIBILITY OF SUCH DAMAGE.
  */
 public class ValidationEngine implements IValidatorResourceFetcher, IPackageInstaller {
 
+  public class ValidationRecord {
+
+    private String location;
+    private List<ValidationMessage> messages;
+    int err = 0;
+    int warn = 0;
+    int info = 0;
+
+    public ValidationRecord(String location, List<ValidationMessage> messages) {
+      this.location = location;
+      this.messages = messages;
+      for (ValidationMessage vm : messages) {
+        if (vm.getLevel().equals(ValidationMessage.IssueSeverity.FATAL)||vm.getLevel().equals(ValidationMessage.IssueSeverity.ERROR))
+          err++;
+        else if (vm.getLevel().equals(ValidationMessage.IssueSeverity.WARNING))
+          warn++;
+        else if (!vm.isSignpost()) {
+          info++;
+        }
+      }
+    }
+
+    public String getLocation() {
+      return location;
+    }
+
+    public List<ValidationMessage> getMessages() {
+      return messages;
+    }
+
+    public int getErr() {
+      return err;
+    }
+
+    public int getWarn() {
+      return warn;
+    }
+
+    public int getInfo() {
+      return info;
+    }
+
+  }
+
   public class TransformSupportServices implements ITransformerServices {
 
     private List<Base> outputs;
@@ -538,7 +591,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
       throw new FHIRException("Unable to fetch content from "+src+" ("+errors.toString()+")");
 
     }
-    FhirFormat fmt = checkIsResource(cnt, src);
+    FhirFormat fmt = checkFormat(cnt, src);
     if (fmt != null) {
       Map<String, byte[]> res = new HashMap<String, byte[]>();
       res.put(Utilities.changeFileExt(src, "."+fmt.getExtension()), cnt);
@@ -809,33 +862,99 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
     this.noInvariantChecks = value;
   }
 
+  private FhirFormat checkFormat(byte[] cnt, String filename) {
+    System.out.println("   ..Detect format for "+filename);
+    try {
+      JsonTrackingParser.parseJson(cnt);
+      return FhirFormat.JSON;
+    } catch (Exception e) {
+      if (debug) {
+        System.out.println("Not JSON: "+e.getMessage());
+      }
+    }
+    try {
+      parseXml(cnt);
+      return FhirFormat.XML;
+    } catch (Exception e) {
+      if (debug) {
+        System.out.println("Not XML: "+e.getMessage());
+      }
+    }
+    try {
+      new Turtle().parse(TextFile.bytesToString(cnt));
+      return FhirFormat.TURTLE;
+    } catch (Exception e) {
+      if (debug) {
+        System.out.println("Not Turtle: "+e.getMessage());
+      }
+    }
+    try {
+      new StructureMapUtilities(context, null, null).parse(TextFile.bytesToString(cnt), null);
+      return FhirFormat.TEXT;
+    } catch (Exception e) {
+      if (debug) {
+        System.out.println("Not Text: "+e.getMessage());
+      }
+    }
+    if (debug)
+      System.out.println("     .. not a resource: "+filename);
+    return null;
+  }
+
+
   private FhirFormat checkIsResource(byte[] cnt, String filename) {
     System.out.println("   ..Detect format for "+filename);
     try {
       Manager.parse(context, new ByteArrayInputStream(cnt), FhirFormat.JSON);
       return FhirFormat.JSON;
     } catch (Exception e) {
+      if (debug) {
+        System.out.println("Not JSON: "+e.getMessage());
+      }
     }
     try {
-      Manager.parse(context, new ByteArrayInputStream(cnt),FhirFormat.XML);
+      parseXml(cnt);
       return FhirFormat.XML;
     } catch (Exception e) {
+      if (debug) {
+        System.out.println("Not XML: "+e.getMessage());
+      }
     }
     try {
       Manager.parse(context, new ByteArrayInputStream(cnt),FhirFormat.TURTLE);
       return FhirFormat.TURTLE;
     } catch (Exception e) {
+      if (debug) {
+        System.out.println("Not Turtle: "+e.getMessage());
+      }
     }
     try {
       new StructureMapUtilities(context, null, null).parse(TextFile.bytesToString(cnt), null);
       return FhirFormat.TEXT;
     } catch (Exception e) {
+      if (debug) {
+        System.out.println("Not Text: "+e.getMessage());
+      }
     }
     if (debug)
       System.out.println("     .. not a resource: "+filename);
     return null;
   }
 
+  private Document parseXml(byte[] cnt) throws ParserConfigurationException, SAXException, IOException {
+    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+    // xxe protection
+    factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
+    factory.setFeature("http://xml.org/sax/features/external-general-entities", false);
+    factory.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
+    factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
+    factory.setXIncludeAware(false);
+    factory.setExpandEntityReferences(false);
+    factory.setNamespaceAware(true);
+    DocumentBuilder builder = factory.newDocumentBuilder();
+    return builder.parse(new ByteArrayInputStream(cnt));
+  }
+
   private FhirFormat checkIsResource(String path) throws IOException {
     String ext = Utilities.getFileExtension(path);
     if (Utilities.existsInList(ext, "xml"))
@@ -1097,7 +1216,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
   public OperationOutcome validate(String source, List<String> profiles) throws FHIRException, IOException {
     List<String> l = new ArrayList<String>();
     l.add(source);
-    return (OperationOutcome)validate(l, profiles);
+    return (OperationOutcome)validate(l, profiles, null);
   }
 
   public List<ScanOutputItem> validateScan(List<String> sources, Set<String> guides) throws FHIRException, IOException, EOperationOutcome {
@@ -1193,7 +1312,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
     }
   }
 
-  public Resource validate(List<String> sources, List<String> profiles) throws FHIRException, IOException {
+  public Resource validate(List<String> sources, List<String> profiles, List<ValidationRecord> record) throws FHIRException, IOException {
     if (profiles.size() > 0) {
       System.out.println("  Profiles: "+profiles);
     }
@@ -1207,7 +1326,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
       System.out.print("  Validate " + ref);
       Content cnt = loadContent(ref, "validate", false);
       try {
-        OperationOutcome outcome = validate(ref, cnt.focus, cnt.cntType, profiles);
+        OperationOutcome outcome = validate(ref, cnt.focus, cnt.cntType, profiles, record);
         ToolingExtensions.addStringExtension(outcome, ToolingExtensions.EXT_OO_FILE, ref);
         System.out.println(" " + context.clock().milestone());
         results.addEntry().setResource(outcome);
@@ -1281,7 +1400,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
   }
 
 
-  public OperationOutcome validate(String location, byte[] source, FhirFormat cntType, List<String> profiles) throws FHIRException, IOException, EOperationOutcome, SAXException {
+  public OperationOutcome validate(String location, byte[] source, FhirFormat cntType, List<String> profiles, List<ValidationRecord> record) throws FHIRException, IOException, EOperationOutcome, SAXException {
     List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
     if (doNative) {
       SchemaValidator.validateSchema(location, cntType, messages);
@@ -1291,6 +1410,9 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
     if (showTimes) {
       System.out.println(location+": "+validator.reportTimes());
     }
+    if (record != null) {
+      record.add(new ValidationRecord(location, messages));
+    }
     return messagesToOutcome(messages);
   }
 

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

@@ -41,6 +41,8 @@ public class CliContext {
   private String map = null;
   @JsonProperty("output")
   private String output = null;
+  @JsonProperty("htmlOutput")
+  private String htmlOutput = null;
   @JsonProperty("txServer")
   private String txServer = "http://tx.fhir.org";
   @JsonProperty("sv")
@@ -252,6 +254,17 @@ public class CliContext {
     return this;
   }
 
+  @JsonProperty("output")
+  public String getHtmlOutput() {
+    return htmlOutput;
+  }
+
+  @JsonProperty("output")
+  public CliContext setHtmlOutput(String htmlOutput) {
+    this.htmlOutput = htmlOutput;
+    return this;
+  }
+
   @JsonProperty("canDoNative")
   public boolean getCanDoNative() {
     return canDoNative;
@@ -472,6 +485,7 @@ public class CliContext {
       noExtensibleBindingMessages == that.noExtensibleBindingMessages &&
       Objects.equals(map, that.map) &&
       Objects.equals(output, that.output) &&
+      Objects.equals(htmlOutput, that.htmlOutput) &&
       Objects.equals(txServer, that.txServer) &&
       Objects.equals(sv, that.sv) &&
       Objects.equals(txLog, that.txLog) &&
@@ -493,7 +507,7 @@ public class CliContext {
 
   @Override
   public int hashCode() {
-    return Objects.hash(doNative, anyExtensionsAllowed, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching, noExtensibleBindingMessages, map, output, txServer, sv, txLog, mapLog, lang, fhirpath, snomedCT, targetVer, igs, questionnaireMode, profiles, sources, mode, locale, locations, crumbTrails, showTimes);
+    return Objects.hash(doNative, anyExtensionsAllowed, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching, noExtensibleBindingMessages, map, output, htmlOutput, txServer, sv, txLog, mapLog, lang, fhirpath, snomedCT, targetVer, igs, questionnaireMode, profiles, sources, mode, locale, locations, crumbTrails, showTimes);
   }
 
   @Override
@@ -510,6 +524,7 @@ public class CliContext {
       ", noExtensibleBindingMessages=" + noExtensibleBindingMessages +
       ", map='" + map + '\'' +
       ", output='" + output + '\'' +
+      ", htmlOutput='" + htmlOutput + '\'' +
       ", txServer='" + txServer + '\'' +
       ", sv='" + sv + '\'' +
       ", txLog='" + txLog + '\'' +

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

@@ -0,0 +1,181 @@
+package org.hl7.fhir.validation.cli.services;
+
+import java.text.DateFormat;
+import java.util.Date;
+import java.util.List;
+
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
+import org.hl7.fhir.validation.ValidationEngine.ValidationRecord;
+import org.hl7.fhir.validation.cli.utils.VersionUtil;
+
+public class HTMLOutputGenerator {
+
+  private List<ValidationRecord> records;
+
+  public HTMLOutputGenerator(List<ValidationRecord> records) {
+    super();
+    this.records = records;
+  }
+  
+  public String generate(long time) {
+    
+    StringBuilder b = new StringBuilder();
+    b.append(genHeader(time));
+    int i = 0;
+    for (ValidationRecord f : records) {
+      i++;
+      b.append(genSummaryRow(i, f));
+    }
+    b.append("</table>\r\n");
+
+    i = 0;
+    int id = 0;
+    for (ValidationRecord f : records) {
+      i++;
+      b.append(genStart(i, f));
+      if (f.getMessages().size() > 0) {
+        b.append(
+            " <table class=\"grid\">\r\n"+
+                "   <tr>\r\n"+
+                "     <td><b>Path</b></td><td><b>Severity</b></td><td><b>Message</b></td>\r\n"+
+            "   </tr>\r\n");
+        for (ValidationMessage vm : f.getMessages()) {
+          id++;
+          b.append(genDetails(vm, "m"+id));
+        }
+        b.append("</table>\r\n");
+      } else {
+        b.append("<p>No Issues detected</p>\r\n");
+      }
+    }
+    return b.toString();
+  }    
+   
+  private String genHeader(long time) {
+    int err = 0;
+    int warn = 0;
+    int info = 0;
+    for (ValidationRecord f : records) {
+      err = err + f.getErr();
+      warn = warn + f.getWarn();
+      info = info + f.getInfo();
+    }
+
+    return 
+        "<!DOCTYPE HTML>\r\n"+
+        "<html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\">\r\n"+
+        "<head>\r\n"+
+        "  <title>Validation Results</title>\r\n"+
+        "  <link href=\"http://hl7.org/fhir/fhir.css\" rel=\"stylesheet\"/>\r\n"+
+        "  <style>\r\n"+
+        "    span.flip  { background-color: #4CAF50; color: white; border: solid 1px #a6d8a8; padding: 2px }\r\n"+
+        "  </style>\r\n"+
+        "  <script>\r\n"+
+        "    function flip(id) {\r\n"+
+        "      var span = document.getElementById('s'+id);\r\n"+
+        "      var div = document.getElementById(id);\r\n"+
+        "      if (document.getElementById('s'+id).innerHTML == 'Show Reasoning') {\r\n"+
+        "        div.style.display = 'block';\r\n"+
+        "        span.innerHTML = 'Hide Reasoning';\r\n"+
+        "      } else {\r\n"+
+        "        div.style.display = 'none';\r\n"+
+        "        span.innerHTML = 'Show Reasoning';\r\n"+
+        "      }\r\n"+
+        "    }\r\n"+
+        "  </script>\r\n"+
+        "</head>\r\n"+
+        "<body style=\"margin: 20px; background-color: #ffffff\">\r\n"+
+        " <h1>Validation Results</h1>\r\n"+
+        " <p>"+err+" "+Utilities.pluralize("error", err)+", "+warn+" "+Utilities.pluralize("warning", warn)+", "+info+" "+Utilities.pluralize("hint", info)+". Generated "+now()+" by Validator "+VersionUtil.getVersionString()+" ("+time+"ms)</p>\r\n"+
+        " <table class=\"grid\">\r\n"+
+        "   <tr>\r\n"+
+        "     <td><b>Filename</b></td><td><b>Errors</b></td><td><b>Warnings</b></td><td><b>Hints</b></td>\r\n"+
+        "   </tr>\r\n";
+  }
+
+  private String now() {
+    return DateFormat.getDateTimeInstance().format(new Date());
+  }
+
+  private String genSummaryRow(int i, ValidationRecord rec) {
+    String color = colorForLevel(IssueSeverity.ERROR, false);
+    if (rec.getErr() == 0) {
+      color = "#EFFFEF";
+    }       
+    return       
+        "   <tr style=\"background-color: "+color+"\">\r\n"+
+        "     <td><a href=\"#;"+i+"\"><b>"+Utilities.escapeXml(rec.getLocation())+"</b></a></td><td><b>"+rec.getErr()+"</b></td><td><b>"+rec.getWarn()+"</b></td><td><b>"+rec.getInfo()+"</b></td>\r\n"+
+        "   </tr>\r\n";
+  }
+
+  private String genStart(int i, ValidationRecord f) {
+    String xlink = Utilities.isAbsoluteUrl(f.getLocation()) ? f.getLocation() : "file:"+f.getLocation();
+    return 
+        "<hr/>\r\n"+
+        "<a name=\"l"+i+"\"> </a>\r\n"+
+        "<h2><a href=\""+xlink+"\">"+Utilities.escapeXml(f.getLocation())+"</a></h2>\r\n";
+  }
+  
+  
+  private String genDetails(ValidationMessage vm, String id) {
+    String path = vm.getLocation() == null ? "" : vm.getLocation()+ lineCol(vm); 
+    String level = vm.isSlicingHint() ? "Slicing Information" : vm.isSignpost() ? "Process Info" : vm.getLevel().toCode();
+    String color = colorForLevel(vm.getLevel(), vm.isSignpost());
+    String mid = vm.getMessageId();
+    String msg = vm.getHtml();
+    String msgdetails = vm.isSlicingHint() ? vm.getSliceHtml() : vm.getHtml();
+    if (vm.isSlicingHint()) {
+      return 
+          "   <tr style=\"background-color: "+color+"\">\r\n"+
+          "     <td><b>"+path+"</b></td><td><b>"+level+"</b></td><td><b>"+msg+"</b> <span id=\"s"+id+"\" class=\"flip\" onclick=\"flip('"+id+"')\">Show Reasoning</span><div id=\""+id+"\" style=\"display: none\"><p>&nbsp;</p>"+msgdetails+"</div></td>\r\n"+
+          "   </tr>\r\n";
+          
+    } else {
+      return 
+          "   <tr style=\"background-color: "+color+"\">\r\n"+
+          "     <td><b>"+path+"</b></td><td><b>"+level+"</b></td><td title=\""+mid+"\"><b>"+msg+"</b></td>\r\n"+
+          "   </tr>\r\n";
+    }
+  }
+  
+  private String lineCol(ValidationMessage vm) {
+    return vm.getLine() > 0 ? " (l"+vm.getLine()+"/c"+vm.getCol()+")" : "";
+  }
+  
+
+  private String colorForLevel(IssueSeverity level, boolean signpost) {
+    if (signpost) {
+      return "#d6feff";
+    }
+    switch (level) {
+    case ERROR:
+      return "#ffcccc";
+    case FATAL:
+      return "#ff9999";
+    case WARNING:
+      return "#ffebcc";
+    default: // INFORMATION:
+      return "#ffffe6";
+    }
+  }
+
+  private String halfColorForLevel(IssueSeverity level, boolean signpost) {
+    if (signpost) {
+      return "#e3feff";
+    }
+    switch (level) {
+    case ERROR:
+      return "#ffeeee";
+    case FATAL:
+      return "#ffcccc";
+    case WARNING:
+      return "#fff4ee";
+    default: // INFORMATION:
+      return "#fffff2";
+    }
+  }
+
+
+}

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

@@ -27,6 +27,7 @@ import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.validation.ValidationEngine;
+import org.hl7.fhir.validation.ValidationEngine.ValidationRecord;
 import org.hl7.fhir.validation.cli.model.*;
 import org.hl7.fhir.validation.cli.utils.EngineMode;
 import org.hl7.fhir.validation.cli.utils.VersionSourceInformation;
@@ -69,7 +70,9 @@ public class ValidationService {
   }
   
   public static void validateSources(CliContext cliContext, ValidationEngine validator) throws Exception {
-    Resource r = validator.validate(cliContext.getSources(), cliContext.getProfiles());
+    long start = System.currentTimeMillis();
+    List<ValidationRecord> records = new ArrayList<>();
+    Resource r = validator.validate(cliContext.getSources(), cliContext.getProfiles(), records);
     int ec = 0;
     System.out.println("Done. "+validator.getContext().clock().report());
     System.out.println();
@@ -92,6 +95,11 @@ public class ValidationService {
       x.compose(s, r);
       s.close();
     }
+    if (cliContext.getHtmlOutput() != null) {
+      String html = new HTMLOutputGenerator(records).generate(System.currentTimeMillis()-start);
+      TextFile.stringToFile(html, cliContext.getHtmlOutput());
+      System.out.println("HTML Summary in "+cliContext.getHtmlOutput());
+    }
     System.exit(ec > 0 ? 1 : 0);
   }
 
@@ -288,10 +296,12 @@ public class ValidationService {
     System.out.println("Scanning for versions (no -version parameter):");
     VersionSourceInformation versions = ValidationService.scanForVersions(cliContext);
     for (String s : versions.getReport()) {
+      if (!s.equals("(nothing found)")) {
         System.out.println("  " + s);
       }
+    }
     if (versions.isEmpty()) {
-      System.out.println("-> Using Default version '" + VersionUtilities.CURRENT_VERSION + "'");
+      System.out.println("  No Version Info found: Using Default version '" + VersionUtilities.CURRENT_VERSION + "'");
       return "current";
     }
     if (versions.size() == 1) {

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

@@ -12,6 +12,7 @@ public class Params {
 
   public static final String VERSION = "-version";
   public static final String OUTPUT = "-output";
+  public static final String HTML_OUTPUT = "-html-output";
   public static final String PROXY = "-proxy";
   public static final String PROFILE = "-profile";
   public static final String BUNDLE = "-bundle";
@@ -93,6 +94,11 @@ public class Params {
           throw new Error("Specified -output without indicating output file");
         else
           cliContext.setOutput(args[++i]);
+      } else if (args[i].equals(HTML_OUTPUT)) {
+        if (i + 1 == args.length)
+          throw new Error("Specified -html-output without indicating output file");
+        else
+          cliContext.setHtmlOutput(args[++i]);
       } else if (args[i].equals(PROXY)) {
         i++; // ignore next parameter
       } else if (args[i].equals(PROFILE)) {

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

@@ -961,7 +961,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     } else {
       if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() == fixed.getCoding().size(), I18nConstants.TERMINOLOGY_TX_CODING_COUNT, Integer.toString(fixed.getCoding().size()), Integer.toString(codings.size()))) {
         for (int i = 0; i < codings.size(); i++)
-          checkFixedValue(errors, path + ".coding", codings.get(i), fixed.getCoding().get(i), fixedSource, "coding", focus);
+          checkFixedValue(errors, path + ".coding", codings.get(i), fixed.getCoding().get(i), fixedSource, "coding", focus, false);
       }
     }
   }
@@ -1748,10 +1748,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return b.toString();
   }
 
-  private void checkFixedValue(List<ValidationMessage> errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String fixedSource, String propName, Element parent) {
-    checkFixedValue(errors, path, focus, fixed, fixedSource, propName, parent, false);
-  }
-
   @SuppressWarnings("rawtypes")
   private void checkFixedValue(List<ValidationMessage> errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String fixedSource, String propName, Element parent, boolean pattern) {
     if ((fixed == null || fixed.isEmpty()) && focus == null) {
@@ -1829,7 +1825,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         for (Extension e : fixed.getExtension()) {
           Element ex = getExtensionByUrl(extensions, e.getUrl());
           if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, ex != null, I18nConstants.EXTENSION_EXT_COUNT_NOTFOUND, e.getUrl())) {
-            checkFixedValue(errors, path, ex.getNamedChild("extension").getNamedChild("value"), e.getValue(), fixedSource, "extension.value", ex.getNamedChild("extension"));
+            checkFixedValue(errors, path, ex.getNamedChild("extension").getNamedChild("value"), e.getValue(), fixedSource, "extension.value", ex.getNamedChild("extension"), false);
           }
         }
       }
@@ -1842,27 +1838,35 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), fixedSource, "period", focus, pattern);
 
     List<Element> parts = new ArrayList<Element>();
+    if (!pattern || fixed.hasFamily()) {
       focus.getNamedChildren("family", parts);
       if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() > 0 == fixed.hasFamily(), I18nConstants.FIXED_TYPE_CHECKS_DT_NAME_FAMILY, (fixed.hasFamily() ? "1" : "0"), Integer.toString(parts.size()))) {
         for (int i = 0; i < parts.size(); i++)
           checkFixedValue(errors, path + ".family", parts.get(i), fixed.getFamilyElement(), fixedSource, "family", focus, pattern);
       }
+    }
+    if (!pattern || fixed.hasGiven()) {
       focus.getNamedChildren("given", parts);
       if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getGiven().size(), I18nConstants.FIXED_TYPE_CHECKS_DT_NAME_GIVEN, Integer.toString(fixed.getGiven().size()), Integer.toString(parts.size()))) {
         for (int i = 0; i < parts.size(); i++)
           checkFixedValue(errors, path + ".given", parts.get(i), fixed.getGiven().get(i), fixedSource, "given", focus, pattern);
       }
+    }
+    if (!pattern || fixed.hasPrefix()) {
       focus.getNamedChildren("prefix", parts);
       if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getPrefix().size(), I18nConstants.FIXED_TYPE_CHECKS_DT_NAME_PREFIX, Integer.toString(fixed.getPrefix().size()), Integer.toString(parts.size()))) {
         for (int i = 0; i < parts.size(); i++)
           checkFixedValue(errors, path + ".prefix", parts.get(i), fixed.getPrefix().get(i), fixedSource, "prefix", focus, pattern);
       }
+    }
+    if (!pattern || fixed.hasSuffix()) {
       focus.getNamedChildren("suffix", parts);
       if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getSuffix().size(), I18nConstants.FIXED_TYPE_CHECKS_DT_NAME_SUFFIX, Integer.toString(fixed.getSuffix().size()), Integer.toString(parts.size()))) {
         for (int i = 0; i < parts.size(); i++)
           checkFixedValue(errors, path + ".suffix", parts.get(i), fixed.getSuffix().get(i), fixedSource, "suffix", focus, pattern);
       }
     }
+  }
 
   private void checkIdentifier(List<ValidationMessage> errors, String path, Element element, ElementDefinition context) {
     String system = element.getNamedChildValue("system");
@@ -3054,9 +3058,22 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       // work back through the parent list.
       // really, there should only be one level for this (contained resources cannot contain
       // contained resources), but we'll leave that to some other code to worry about
+      boolean wasContained = false;
       while (stack != null && stack.getElement() != null) {
         if (stack.getElement().getProperty().isResource()) {
           // ok, we'll try to find the contained reference
+          if (ref.equals("#") && stack.getElement().getSpecial() != SpecialElement.CONTAINED && wasContained) {
+            ResolvedReference rr = new ResolvedReference();
+            rr.setResource(stack.getElement());
+            rr.setFocus(stack.getElement());
+            rr.setExternal(false);
+            rr.setStack(stack.push(stack.getElement(), -1, stack.getElement().getProperty().getDefinition(), stack.getElement().getProperty().getDefinition()));
+            rr.getStack().qualifyPath(".ofType("+stack.getElement().fhirType()+")");
+            return rr;            
+          }
+          if (stack.getElement().getSpecial() == SpecialElement.CONTAINED) {
+            wasContained = true;
+          }
           IndexedElement res = getContainedById(stack.getElement(), ref.substring(1));
           if (res != null) {
             ResolvedReference rr = new ResolvedReference();
@@ -4069,8 +4086,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     
     // check type invariants
     checkInvariants(hostContext, errors, profile, definition, resource, element, stack, false);
-    if (definition.getFixed() != null)
+    if (definition.getFixed() != null) {
-      checkFixedValue(errors, stack.getLiteralPath(), element, definition.getFixed(), profile.getUrl(), definition.getSliceName(), null);
+      checkFixedValue(errors, stack.getLiteralPath(), element, definition.getFixed(), profile.getUrl(), definition.getSliceName(), null, false);
+    } 
+    if (definition.getPattern() != null) {
+      checkFixedValue(errors, stack.getLiteralPath(), element, definition.getPattern(), profile.getUrl(), definition.getSliceName(), null, true);
+    } 
 
     // get the list of direct defined children, including slices
     List<ElementDefinition> childDefinitions = profileUtilities.getChildMap(profile, definition);
@@ -4136,13 +4157,20 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, ElementInfo ei, String extensionUrl)
     throws FHIRException, DefinitionException {
 
+    if (debug && ei.definition != null && ei.slice != null) {
+      System.out.println(Utilities.padLeft("", ' ', stack.depth())+ "Check "+ei.getPath()+" against both "+ei.definition.getId()+" and "+ei.slice.getId());
+    }
     if (ei.definition != null) {
-      checkChildByDefinition(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei,
+      if (debug) {
-          extensionUrl, ei.definition, false);
+        System.out.println(Utilities.padLeft("", ' ', stack.depth())+ "Check "+ei.getPath()+" against defn "+ei.definition.getId());
+      }
+      checkChildByDefinition(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei, extensionUrl, ei.definition, false);
     }
     if (ei.slice != null) {
-      checkChildByDefinition(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei,
+      if (debug) {
-          extensionUrl, ei.slice, true);
+        System.out.println(Utilities.padLeft("", ' ', stack.depth())+ "Check "+ei.getPath()+" against slice "+ei.slice.getId());
+      }
+      checkChildByDefinition(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei, extensionUrl, ei.slice, true);
     }
   }
 
@@ -4186,11 +4214,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     } else if (checkDefn.getType().size() > 1) {
 
       String prefix = tail(checkDefn.getPath());
-      assert typesAreAllReference(checkDefn.getType()) || checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") : prefix;
+      assert typesAreAllReference(checkDefn.getType()) || checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") || isResourceAndTypes(checkDefn) : "Multiple Types allowed, but name is wrong @ "+checkDefn.getPath()+": "+checkDefn.typeSummaryVB();
 
-      if (checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR))
+      if (checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR)) {
         type = ei.getElement().getType();
-      else {
+      } else if (ei.getElement().isResource()) {
+        type = ei.getElement().fhirType();            
+      } else {
         prefix = prefix.substring(0, prefix.length() - 3);
         for (TypeRefComponent t : checkDefn.getType())
           if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) {
@@ -4251,7 +4281,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         checkPrimitive(hostContext, errors, ei.getPath(), type, checkDefn, ei.getElement(), profile, stack);
       } else {
         if (checkDefn.hasFixed()) {
-          checkFixedValue(errors, ei.getPath(), ei.getElement(), checkDefn.getFixed(), profile.getUrl(), checkDefn.getSliceName(), null);
+          checkFixedValue(errors, ei.getPath(), ei.getElement(), checkDefn.getFixed(), profile.getUrl(), checkDefn.getSliceName(), null, false);
         }
         if (checkDefn.hasPattern()) {
           checkFixedValue(errors, ei.getPath(), ei.getElement(), checkDefn.getPattern(), profile.getUrl(), checkDefn.getSliceName(), null, true);
@@ -4386,6 +4416,18 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
   }
 
+  private boolean isResourceAndTypes(ElementDefinition ed) {
+    if (!Utilities.existsInList(ed.getBase().getPath(), "Bundle.entry.resource", "Bundle.entry.response.outcome", "DomainResource.contained", "Parameters.parameter.resource", "Parameters.parameter.part.resource")) {
+      return false;
+    }
+    for (TypeRefComponent tr : ed.getType()) {
+      if (!isResource(tr.getCode())) {
+        return false;
+      }
+    }
+    return true;
+  }
+
   private boolean isResource(String type) {
     StructureDefinition sd = context.fetchTypeDefinition(type);
     return sd != null && sd.getKind().equals(StructureDefinitionKind.RESOURCE);
@@ -4476,18 +4518,18 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
               }
             }
           }
-        String location = "Profile " + profile.getUrl() + ", Element '" + stack.getLiteralPath() + "." + tail(ed.getPath()) + (ed.hasSliceName() ? "[" + ed.getSliceName() + (ed.hasLabel() ? " (" + ed.getLabel() + ")" : "") + "]" : "") + "'";
         if (ed.getMin() > 0) {
           if (problematicPaths.contains(ed.getPath()))
-            hint(errors, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), I18nConstants.VALIDATION_VAL_PROFILE_NOCHECKMIN, location, Integer.toString(ed.getMin()));
+            hint(errors, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), I18nConstants.VALIDATION_VAL_PROFILE_NOCHECKMIN, profile.getUrl(), ed.getPath(), ed.getId(), ed.getSliceName(),ed.getLabel(), stack.getLiteralPath(), Integer.toString(ed.getMin()));
           else
-            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), I18nConstants.VALIDATION_VAL_PROFILE_MINIMUM, location, Integer.toString(ed.getMin()), Integer.toString(count));
+            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), I18nConstants.VALIDATION_VAL_PROFILE_MINIMUM, profile.getUrl(), ed.getPath(), ed.getId(), ed.getSliceName(),ed.getLabel(), stack.getLiteralPath(), Integer.toString(ed.getMin()), Integer.toString(count));
         }
         if (ed.hasMax() && !ed.getMax().equals("*")) {
           if (problematicPaths.contains(ed.getPath()))
-            hint(errors, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()), I18nConstants.VALIDATION_VAL_PROFILE_NOCHECKMAX, location, ed.getMax());
+            hint(errors, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()), I18nConstants.VALIDATION_VAL_PROFILE_NOCHECKMAX, profile.getUrl(), ed.getPath(), ed.getId(), ed.getSliceName(),ed.getLabel(), stack.getLiteralPath(), ed.getMax());
-          else
+          else if (count > Integer.parseInt(ed.getMax())) {
-            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()), I18nConstants.VALIDATION_VAL_PROFILE_MAXIMUM, location, ed.getMax(), Integer.toString(count));
+            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_MAXIMUM, profile.getUrl(), ed.getPath(), ed.getId(), ed.getSliceName(),ed.getLabel(), stack.getLiteralPath(), ed.getMax(), Integer.toString(count));
+          }
         }
       }
     }
@@ -4863,7 +4905,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   private boolean valueMatchesCriteria(Element value, ElementDefinition criteria, StructureDefinition profile) throws FHIRException {
     if (criteria.hasFixed()) {
       List<ValidationMessage> msgs = new ArrayList<ValidationMessage>();
-      checkFixedValue(msgs, "{virtual}", value, criteria.getFixed(), profile.getUrl(), "value", null);
+      checkFixedValue(msgs, "{virtual}", value, criteria.getFixed(), profile.getUrl(), "value", null, false);
       return msgs.size() == 0;
     } else if (criteria.hasBinding() && criteria.getBinding().getStrength() == BindingStrength.REQUIRED && criteria.getBinding().hasValueSet()) {
       throw new FHIRException(context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SLICE_MATCHING__SLICE_MATCHING_BY_VALUE_SET_NOT_DONE));
@@ -4983,6 +5025,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     if ("(component.empty() and related.empty()) implies (dataAbsentReason or value)".equals(expr))
       return "(component.empty() and related.empty()) implies (dataAbsentReason.exists() or value.exists())";
 
+    if ("reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))".equals(expr)) {
+      return "(reference = '#') or reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))";
+    }
+    if ("reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))".equals(expr)) {
+      return "(reference = '#') or reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))";
+    }
     if ("".equals(expr))
       return "";
     return expr;

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

@@ -165,11 +165,25 @@ public class StructureDefinitionValidator extends BaseValidator {
       if (t == null) {
         rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), code.equals(t), I18nConstants.SD_ED_TYPE_PROFILE_NOTYPE, p);
       } else {
-        rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), code.equals(t), I18nConstants.SD_ED_TYPE_PROFILE_WRONG, p, t, code);
+        rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), isInstanceOf(t, code), I18nConstants.SD_ED_TYPE_PROFILE_WRONG, p, t, code);
       }
     }
   }
 
+  private boolean isInstanceOf(String t, String code) {
+    StructureDefinition sd = context.fetchTypeDefinition(t);
+    while (sd != null) {
+      if (sd.getType().equals(code)) {
+        return true;
+      }
+      sd = sd.hasBaseDefinition() ? context.fetchResource(StructureDefinition.class, sd.getBaseDefinition()) : null;
+      if (sd != null && !sd.getAbstract()) {
+        sd = null;
+      }
+    }
+    return false;
+  }
+
   private String determineBaseType(StructureDefinition sd) {
     while (sd != null && !sd.hasType() && sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
       sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());

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

@@ -187,5 +187,13 @@ public class NodeStack {
     return literalPath;
   }
 
+  public int depth() {
+    if (parent == null) {
+      return 0;
+    } else {
+      return parent.depth()+1;
+    }
+  }
+
 
 }

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

@@ -90,7 +90,7 @@ public class ValidationEngineTests {
     }
     if (!org.hl7.fhir.validation.tests.utilities.TestUtilities.silent)
       System.out.println("Test102: Validate patient-example.xml in v1.0.2 version");
-    ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, "41.0.2");
+    ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, "1.0.2");
     ve.setNoInvariantChecks(true);
     OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient102.xml"), null);
     if (!TestUtilities.silent)

pom.xml

@@ -19,7 +19,7 @@
 
     <properties>
         <hapi_fhir_version>5.1.0</hapi_fhir_version>
-        <validator_test_case_version>1.1.46</validator_test_case_version>
+        <validator_test_case_version>1.1.47-SNAPSHOT</validator_test_case_version>
         <junit_jupiter_version>5.6.2</junit_jupiter_version>
         <maven_surefire_version>3.0.0-M4</maven_surefire_version>
         <jacoco_version>0.8.5</jacoco_version>