Merge pull request #940 from hapifhir/gg-202210-coding-validation

Gg 202210 coding validation

org.hl7.fhir.core.generator/configuration/CodeableConcept.java

@@ -93,4 +93,9 @@ public boolean hasCoding(String system, String code) {
   public void addCoding(String system, String code, String display) {
     getCoding().add(new Coding(system, code, display));
   }
-  
+  
+  @Override 
+  public String toString() { 
+    return hasCoding() ? getCoding().toString() : "["+getText()+"]"; 
+  } 
+   

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

@@ -365,8 +365,9 @@ public class XmlParser extends ParserBase {
           } else
             ok = ok || (attr.getLocalName().equals("schemaLocation")); // xsi:schemalocation allowed for non FHIR content
           ok = ok || (hasTypeAttr(element) && attr.getLocalName().equals("type") && FormatUtilities.NS_XSI.equals(attr.getNamespaceURI())); // xsi:type allowed if element says so
-          if (!ok)  
+          if (!ok) { 
             logError(line(node, false), col(node, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ATTRIBUTE__ON__FOR_TYPE__PROPERTIES__, attr.getNodeName(), node.getNodeName(), element.fhirType(), properties), IssueSeverity.ERROR);
+          }
       	}
     	}
     }

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

@@ -404,6 +404,11 @@ public boolean hasCoding(String system, String code) {
   public void addCoding(String system, String code, String display) {
     getCoding().add(new Coding(system, code, display));
   }
+
+  @Override
+  public String toString() {
+    return hasCoding() ? getCoding().toString() : "["+getText()+"]";
+  }
   
 // end addition
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetChecker.java

@@ -1,5 +1,6 @@
 package org.hl7.fhir.r5.terminologies;
 
+import java.util.ArrayList;
 import java.util.List;
 
 /*
@@ -34,10 +35,24 @@ import java.util.List;
 
 
 import org.hl7.fhir.r5.terminologies.ValueSetExpander.ETooCostly;
+import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
 import org.hl7.fhir.r5.utils.EOperationOutcome;
 
 public interface ValueSetChecker {
 
-  Boolean codeInValueSet(String system, String code, List<String> warnings) throws ETooCostly, EOperationOutcome, Exception;
+  public static class ValidationProcessInfo {
+    private TerminologyServiceErrorClass err;
+    private List<String> warnings = new ArrayList<>();
+    public TerminologyServiceErrorClass getErr() {
+      return err;
+    }
+    public void setErr(TerminologyServiceErrorClass err) {
+      this.err = err;
+    }
+    public List<String> getWarnings() {
+      return warnings;
+    }
+  }
+  Boolean codeInValueSet(String system, String code, ValidationProcessInfo info) throws ETooCostly, EOperationOutcome, Exception;
 
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java

@@ -61,6 +61,7 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceDesignationComponent;
 import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.r5.terminologies.ValueSetChecker.ValidationProcessInfo;
 import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
@@ -129,11 +130,11 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
   public ValidationResult validateCode(CodeableConcept code) throws FHIRException {
     // first, we validate the codings themselves
     List<String> errors = new ArrayList<String>();
-    List<String> warnings = new ArrayList<String>();
+    ValidationProcessInfo info = new ValidationProcessInfo();
     if (options.getValueSetMode() != ValueSetMode.CHECK_MEMERSHIP_ONLY) {
       for (Coding c : code.getCoding()) {
         if (!c.hasSystem()) {
-          warnings.add(context.formatMessage(I18nConstants.CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE));
+          info.getWarnings().add(context.formatMessage(I18nConstants.CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE));
         }
         CodeSystem cs = resolveCodeSystem(c.getSystem());
         ValidationResult res = null;
@@ -145,7 +146,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
         if (!res.isOk()) {
           errors.add(res.getMessage());
         } else if (res.getMessage() != null) {
-          warnings.add(res.getMessage());
+          info.getWarnings().add(res.getMessage());
         }
       }
     }
@@ -153,7 +154,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
     if (valueset != null && options.getValueSetMode() != ValueSetMode.NO_MEMBERSHIP_CHECK) {
       Boolean result = false;
       for (Coding c : code.getCoding()) {
-        Boolean ok = codeInValueSet(c.getSystem(), c.getCode(), warnings);
+        Boolean ok = codeInValueSet(c.getSystem(), c.getCode(), info);
         if (ok == null && result == false) {
           result = null;
         } else if (ok) {
@@ -162,15 +163,15 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
         }
       }
       if (result == null) {
-        warnings.add(0, context.formatMessage(I18nConstants.UNABLE_TO_CHECK_IF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));        
+        info.getWarnings().add(0, context.formatMessage(I18nConstants.UNABLE_TO_CHECK_IF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));        
       } else if (!result) {
         errors.add(0, context.formatMessage(I18nConstants.NONE_OF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));
       }
     }
     if (errors.size() > 0) {
       return new ValidationResult(IssueSeverity.ERROR, errors.toString());
-    } else if (warnings.size() > 0) {
+    } else if (info.getWarnings().size() > 0) {
-      return new ValidationResult(IssueSeverity.WARNING, warnings.toString());
+      return new ValidationResult(IssueSeverity.WARNING, info.getWarnings().toString());
     } else {
       ConceptDefinitionComponent cd = new ConceptDefinitionComponent(foundCoding.getCode());
       cd.setDisplay(foundCoding.getDisplay());
@@ -251,19 +252,24 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
       inInclude = checkInclude(code);
     }
 
-    List<String> warnings = new ArrayList<>();
+    ValidationProcessInfo info = new ValidationProcessInfo();
     
     // then, if we have a value set, we check it's in the value set
     if (valueset != null && options.getValueSetMode() != ValueSetMode.NO_MEMBERSHIP_CHECK) {
       if ((res==null || res.isOk())) { 
-        Boolean ok = codeInValueSet(system, code.getCode(), warnings);
+        Boolean ok = codeInValueSet(system, code.getCode(), info);
         if (ok == null || !ok) {
           if (res == null) {
             res = new ValidationResult((IssueSeverity) null, null);
           }
-          if (!inExpansion && !inInclude) {
+          if (info.getErr() != null) {
-            if (warnings != null) {
+            res.setErrorClass(info.getErr());
-              res.setMessage("Not in value set "+valueset.getUrl()+" ("+warnings+")").setSeverity(IssueSeverity.ERROR);              
+          }
+          if (ok == null) {
+            res.setMessage("Unable to check whether code is in value set "+valueset.getUrl()+": "+info.getWarnings()).setSeverity(IssueSeverity.WARNING);
+          } else if (!inExpansion && !inInclude) {
+            if (!info.getWarnings().isEmpty()) {
+              res.setMessage("Not in value set "+valueset.getUrl()+": "+info.getWarnings()).setSeverity(IssueSeverity.ERROR);              
             } else {
               res.setMessage("Not in value set "+valueset.getUrl()).setSeverity(IssueSeverity.ERROR);
             }
@@ -640,7 +646,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
   }
   
   @Override
-  public Boolean codeInValueSet(String system, String code, List<String> warnings) throws FHIRException {
+  public Boolean codeInValueSet(String system, String code, ValidationProcessInfo info) throws FHIRException {
     if (valueset == null) {
       return false;
     }
@@ -651,7 +657,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
     } else if (valueset.hasCompose()) {
       int i = 0;
       for (ConceptSetComponent vsi : valueset.getCompose().getInclude()) {
-        Boolean ok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, warnings);
+        Boolean ok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, info);
         i++;
         if (ok == null && result == false) {
           result = null;
@@ -662,7 +668,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
       }
       i = valueset.getCompose().getInclude().size();
       for (ConceptSetComponent vsi : valueset.getCompose().getExclude()) {
-        Boolean nok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, warnings);
+        Boolean nok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, info);
         i++;
         if (nok == null && result == false) {
           result = null;
@@ -675,7 +681,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
     return result;
   }
 
-  private Boolean inComponent(ConceptSetComponent vsi, int vsiIndex, String system, String code, boolean only, List<String> warnings) throws FHIRException {
+  private Boolean inComponent(ConceptSetComponent vsi, int vsiIndex, String system, String code, boolean only, ValidationProcessInfo info) throws FHIRException {
     boolean ok = true;
     
     if (vsi.hasValueSet()) {
@@ -721,8 +727,9 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
       vs.getCompose().addInclude(vsi);
       ValidationResult res = context.validateCode(options.noClient(), new Coding(system, code, null), vs);
       if (res.getErrorClass() == TerminologyServiceErrorClass.UNKNOWN || res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED || res.getErrorClass() == TerminologyServiceErrorClass.VALUESET_UNSUPPORTED) {
-        if (warnings != null && res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
+        if (info != null && res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
-          warnings.add(context.formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system));
+          info.getWarnings().add(context.formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system));
+          info.setErr(TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED);
         }
         return null;
       }

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

@@ -4503,7 +4503,18 @@ public class FHIRPathEngine {
         return makeBoolean(false);
       }
     } else if (ns.equals("FHIR")) {
-      return makeBoolean(n.equals(focus.get(0).fhirType()));
+      if (n.equals(focus.get(0).fhirType())) {
+        return makeBoolean(true);
+      } else {
+        StructureDefinition sd = worker.fetchTypeDefinition(focus.get(0).fhirType());
+        while (sd != null) {
+          if (n.equals(sd.getType())) {
+            return makeBoolean(true);
+          }
+          sd = worker.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
+        }
+        return makeBoolean(false);
+      }
     } else { 
       return makeBoolean(false);
     }

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

@@ -103,6 +103,9 @@ public class GraphQLSchemaGenerator {
       if (sd.getKind() == StructureDefinitionKind.COMPLEXTYPE && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
         tl.put(sd.getName(), sd);
       }
+      if (sd.getKind() == StructureDefinitionKind.RESOURCE && sd.getDerivation() != TypeDerivationRule.CONSTRAINT && sd.getAbstract()) {
+        tl.put(sd.getName(), sd);
+      }
     }
     writer.write("# FHIR GraphQL Schema. Version " + version + "\r\n\r\n");
     writer.write("# FHIR Defined Primitive types\r\n");
@@ -290,16 +293,17 @@ public class GraphQLSchemaGenerator {
   }
 
   private void generateType(Map<String, String> existingTypeNames, Writer writer, StructureDefinition sd, EnumSet<FHIROperationType> operations) throws IOException {
-    if (sd.getAbstract()) {
-      return;
-    }
-
     if (operations.contains(FHIROperationType.READ) || operations.contains(FHIROperationType.SEARCH)) {
       List<StringBuilder> list = new ArrayList<>();
       StringBuilder b = new StringBuilder();
       list.add(b);
       b.append("type ");
       b.append(sd.getName());
+      StructureDefinition sdp = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
+      if (sdp != null) {
+        b.append(" implements ");
+        b.append(sdp.getType());
+      }
       b.append(" {\r\n");
       ElementDefinition ed = sd.getSnapshot().getElementFirstRep();
       generateProperties(existingTypeNames, list, b, sd.getName(), sd, ed, "type", "");
@@ -370,7 +374,13 @@ public class GraphQLSchemaGenerator {
       if (suffix)
         b.append(Utilities.capitalize(typeDetails.getWorkingCode()));
       b.append(": ");
-      b.append(n);
+      if (!child.getMax().equals("1")) {
+        b.append("[");
+        b.append(n);
+        b.append("]");
+      } else {
+        b.append(n);
+      }
       if (!child.getPath().endsWith(".id")) {
         b.append("  _");
         b.append(tail(child.getPath(), suffix));

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

@@ -205,6 +205,7 @@ public class ToolingExtensions {
   public static final String EXT_REND_MD = "http://hl7.org/fhir/StructureDefinition/rendering-markdown";
   public static final String EXT_CAP_STMT_EXPECT = "http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation";
   public static final String EXT_ED_HEIRARCHY = "http://hl7.org/fhir/StructureDefinition/elementdefinition-heirarchy";
+  public static final String EXT_SD_DEPENDENCY = "http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies";
 
   // in the tooling IG
   public static final String EXT_BINDING_ADDITIONAL = "http://hl7.org/fhir/tools/StructureDefinition/additional-binding";

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

@@ -611,6 +611,7 @@ public class I18nConstants {
   public static final String VALIDATION_VAL_PROFILE_SIGNPOST = "VALIDATION_VAL_PROFILE_SIGNPOST";
   public static final String VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL = "VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL";
   public static final String VALIDATION_VAL_PROFILE_SIGNPOST_META = "VALIDATION_VAL_PROFILE_SIGNPOST_META";
+  public static final String VALIDATION_VAL_PROFILE_SIGNPOST_DEP = "VALIDATION_VAL_PROFILE_SIGNPOST_DEP";
   public static final String VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM = "VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM";
   public static final String VALIDATION_VAL_PROFILE_SLICEORDER = "Validation_VAL_Profile_SliceOrder";
   public static final String VALIDATION_VAL_PROFILE_OTHER_VERSION = "VALIDATION_VAL_PROFILE_OTHER_VERSION";
@@ -622,6 +623,7 @@ public class I18nConstants {
   public static final String VALIDATION_VAL_PROFILE_WRONGTYPE = "Validation_VAL_Profile_WrongType";
   public static final String VALIDATION_VAL_PROFILE_WRONGTYPE2 = "Validation_VAL_Profile_WrongType2";
   public static final String VALIDATION_VAL_UNKNOWN_PROFILE = "Validation_VAL_Unknown_Profile";
+  public static final String VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED = "VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED";
   
   public static final String VALUESET_INCLUDE_INVALID_CONCEPT_CODE = "VALUESET_INCLUDE_INVALID_CONCEPT_CODE";
   public static final String VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER = "VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER";

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

@@ -236,6 +236,7 @@ Validation_VAL_Profile_Unknown =  Profile reference ''{0}'' has not been checked
 VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY = Profile reference ''{0}'' has not been checked because it is unknown, and the validator is set to not fetch unknown profiles
 VALIDATION_VAL_PROFILE_UNKNOWN_ERROR = Profile reference ''{0}'' has not been checked because it is unknown, and fetching it resulted in the error {1}
 Validation_VAL_Unknown_Profile = Unknown profile {0}
+VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED = Profile {1} identifies {2} as a dependency (using the extension http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies), but this profile could not be found
 XHTML_XHTML_Attribute_Illegal = Illegal attribute name in the XHTML (''{0}'' on ''{1}'')
 XHTML_XHTML_Element_Illegal = Illegal element name in the XHTML (''{0}'')
 XHTML_XHTML_NS_InValid = Wrong namespace on the XHTML (''{0}'', should be ''{1}'')
@@ -536,6 +537,7 @@ VALIDATION_VAL_GLOBAL_PROFILE_UNKNOWN = Global Profile reference ''{0}'' from IG
 VALIDATION_VAL_PROFILE_SIGNPOST_BASE = Validate resource against profile 
 VALIDATION_VAL_PROFILE_SIGNPOST = Validate resource against profile {0}
 VALIDATION_VAL_PROFILE_SIGNPOST_META = Validate resource against profile {0} (per meta)
+VALIDATION_VAL_PROFILE_SIGNPOST_DEP = Validate resource against profile {0} (per http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies in {1})
 VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM = Validate resource against profile {0} - provided as bundle param
 VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL = Validate resource against profile {0} - a global profile in {1}
 ERROR_GENERATING_SNAPSHOT = Error generating Snapshot: {0} (this usually arises from a problem in the differential)

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

@@ -818,15 +818,31 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     setParents(element);
 
     long t = System.nanoTime();
+    NodeStack stack = new NodeStack(context, path, element, validationLanguage);
     if (profiles == null || profiles.isEmpty()) {
-      validateResource(new ValidatorHostContext(appContext, element), errors, element, element, null, resourceIdRule, new NodeStack(context, path, element, validationLanguage).resetIds(), null);
+      validateResource(new ValidatorHostContext(appContext, element), errors, element, element, null, resourceIdRule, stack.resetIds(), null);
     } else {
+      int i = 0;
+      while (i < profiles.size()) {
+        StructureDefinition sd = profiles.get(i);
+        if (sd.hasExtension(ToolingExtensions.EXT_SD_DEPENDENCY)) {
+          for (Extension ext : sd.getExtensionsByUrl(ToolingExtensions.EXT_SD_DEPENDENCY)) {
+            StructureDefinition dep = context.fetchResource( StructureDefinition.class, ext.getValue().primitiveValue());
+            if (dep == null) {
+              warning(errors, IssueType.BUSINESSRULE, element.line(), element.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED, ext.getValue().primitiveValue(), sd.getUrl());                
+            } else if (!profiles.contains(dep)) {
+              profiles.add(dep);
+            }
+          }
+        }
+        i++;
+      }
       for (StructureDefinition defn : profiles) {
-        validateResource(new ValidatorHostContext(appContext, element), errors, element, element, defn, resourceIdRule, new NodeStack(context, path, element, validationLanguage).resetIds(), null);
+        validateResource(new ValidatorHostContext(appContext, element), errors, element, element, defn, resourceIdRule, stack.resetIds(), null);
       }
     }
     if (hintAboutNonMustSupport) {
-      checkElementUsage(errors, element, new NodeStack(context, path, element, validationLanguage));
+      checkElementUsage(errors, element, stack);
     }
     errors.removeAll(messagesToRemove);
     timeTracker.overall(t);
@@ -1217,7 +1233,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                       checkBindings(errors, path, element, stack, valueset, nextCoding);
                     }
                   }
-                  timeTracker.tx(t, "vc "+DataRenderer.display(context, cc));
+                  timeTracker.tx(t, "vc "+cc.toString());
                 }
               }
             } catch (Exception e) {
@@ -1692,6 +1708,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                           txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_14, describeReference(binding.getValueSet(), valueset), getErrorMessage(vr.getMessage()), theSystem+"#"+theCode);
                         }
                       }
+                    } else if (vr != null && vr.getMessage() != null) {
+                      txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage());
                     }
                   } catch (Exception e) {
                     if (STACK_TRACE) e.printStackTrace();
@@ -3713,7 +3731,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   }
 
   private String getErrorMessage(String message) {
-    return message != null ? " (error message = " + message + ")" : "";
+     return message != null ? " (error message = " + message + ")" : "";
   }
 
   public boolean isSuppressLoincSnomedMessages() {
@@ -4517,28 +4535,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
               } else if (!fetcher.fetchesCanonicalResource(this, profile.primitiveValue())) {
                 warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY, profile.primitiveValue());                
               } else {
-                sd = null;
+                sd = lookupProfileReference(errors, element, stack, i, profile, sd);
-                String url = profile.primitiveValue();
-                CanonicalResourceLookupResult cr = crLookups.get(url);
-                if (cr != null) {
-                  if (cr.error != null) {
-                    warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, url, cr.error);                
-                  } else {
-                    sd = (StructureDefinition) cr.resource;
-                  }
-                } else {
-                  try {
-                    sd = (StructureDefinition) fetcher.fetchCanonicalResource(this, url);
-                    crLookups.put(url, new CanonicalResourceLookupResult(sd));
-                  } catch (Exception e) {
-                    if (STACK_TRACE) { e.printStackTrace(); }
-                    crLookups.put(url, new CanonicalResourceLookupResult(e.getMessage()));
-                    warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, profile.primitiveValue(), e.getMessage());                
-                  }
-                  if (sd != null) {
-                    context.cacheResource(sd);
-                  }
-                }
               }
             }
             if (sd != null) {
@@ -4553,6 +4550,27 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
               if (pctOwned) {
                 pct.done();
               }
+              if (sd.hasExtension(ToolingExtensions.EXT_SD_DEPENDENCY)) {
+                for (Extension ext : sd.getExtensionsByUrl(ToolingExtensions.EXT_SD_DEPENDENCY)) {
+                  StructureDefinition sdi = context.fetchResource(StructureDefinition.class, ext.getValue().primitiveValue());
+                  if (sdi == null) {
+                    warning(errors, IssueType.BUSINESSRULE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED, ext.getValue().primitiveValue(), sd.getUrl());                
+                  } else {
+                    if (crumbTrails) {
+                      element.addMessage(signpost(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), I18nConstants.VALIDATION_VAL_PROFILE_SIGNPOST_DEP, sdi.getUrl(), sd.getUrl()));
+                    }
+                    stack.resetIds();
+                    if (pctOwned) {
+                      pct = new PercentageTracker(resource.countDescendents(), resource.fhirType(), sdi.getUrl(), logProgress);
+                    }
+                    startInner(hostContext, errors, resource, element, sdi, stack, false, pct);
+                    if (pctOwned) {
+                      pct.done();
+                    }
+                    
+                  }
+                }
+              }
             }
           }
         }
@@ -4583,6 +4601,32 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
 //    System.out.println("start: "+(System.currentTimeMillis()-st)+" ("+resource.fhirType()+")");
   }
 
+  private StructureDefinition lookupProfileReference(List<ValidationMessage> errors, Element element, NodeStack stack,
+      int i, Element profile, StructureDefinition sd) {
+    String url = profile.primitiveValue();
+    CanonicalResourceLookupResult cr = crLookups.get(url);
+    if (cr != null) {
+      if (cr.error != null) {
+        warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, url, cr.error);                
+      } else {
+        sd = (StructureDefinition) cr.resource;
+      }
+    } else {
+      try {
+        sd = (StructureDefinition) fetcher.fetchCanonicalResource(this, url);
+        crLookups.put(url, new CanonicalResourceLookupResult(sd));
+      } catch (Exception e) {
+        if (STACK_TRACE) { e.printStackTrace(); }
+        crLookups.put(url, new CanonicalResourceLookupResult(e.getMessage()));
+        warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, profile.primitiveValue(), e.getMessage());                
+      }
+      if (sd != null) {
+        context.cacheResource(sd);
+      }
+    }
+    return sd;
+  }
+
 //  private void plog(String msg) {
 //    long n = System.currentTimeMillis();
 //    String elapsed = Utilities.padLeft(Long.toString(n-start), ' ', 5);
@@ -5720,7 +5764,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     boolean ok;
     try {
       long t = System.nanoTime();
-      ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n);
+       ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n);
       timeTracker.fpe(t);
       msg = fpe.forLog();
     } catch (Exception ex) {

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

@@ -45,6 +45,13 @@ public class FHIRPathExpressionFixer {
       return ("name.exists() implies name.matches('[A-Z]([A-Za-z0-9_]){0,254}')");
     }
     
+    // R5 ballot
+    if (expr.equals("url.matches('([^|#])*')")) {
+      return ("$this.matches('([^|#])*')");
+    }
+    
+    
+    
     
     // clarification in FHIRPath spec
     if ("eld-19".equals(key)) {

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/r5/test/GeneralTests.java

@@ -0,0 +1,36 @@
+package org.hl7.fhir.r5.test;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.hl7.fhir.r5.elementmodel.ParserBase.ValidationPolicy;
+import org.hl7.fhir.r5.model.CodeSystem;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.junit.jupiter.api.Test;
+
+
+public class GeneralTests {
+
+  @Test
+  void testXMLParse() throws IOException {
+    System.out.println(System.getProperty("java.vm.name"));
+    InputStream stream = TestingUtilities.loadTestResourceStream("validator",
+      "xml_v10.xml");
+    org.hl7.fhir.r5.elementmodel.XmlParser xp = new org.hl7.fhir.r5.elementmodel.XmlParser(TestingUtilities.getSharedWorkerContext());
+    xp.setAllowXsiLocation(true);
+    List<ValidationMessage> errorList = new ArrayList<>();
+    xp.setupValidation(ValidationPolicy.EVERYTHING, errorList);
+    try {
+      Object resource = xp.parse(stream);
+    } catch (Exception e) {
+      e.printStackTrace();
+    }
+    for (ValidationMessage message : errorList) {
+      System.out.println(message.getMessage());
+    }
+  }
+  
+}

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

@@ -419,7 +419,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
 
   private void checkOutcomes(List<ValidationMessage> errors, JsonObject focus, String profile, String name) throws IOException {
     JsonObject java = focus.getAsJsonObject("java");
-    OperationOutcome goal = (OperationOutcome) new JsonParser().parse(java.getAsJsonObject("outcome"));
+    OperationOutcome goal = java.has("outcome") ? (OperationOutcome) new JsonParser().parse(java.getAsJsonObject("outcome")) : new OperationOutcome();
     OperationOutcome actual = OperationOutcomeUtilities.createOutcomeSimple(errors);
     actual.setText(null);
     String json = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(actual);
@@ -521,8 +521,10 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
       if (java.has("outcome")) {
         java.remove("outcome");
       }
-      JsonObject oj = JsonTrackingParser.parse(json, null);
+      if (actual.hasIssue()) {
-      java.add("outcome", oj);
+        JsonObject oj = JsonTrackingParser.parse(json, null);
+        java.add("outcome", oj);
+      }
     }
   }