report slicing information automatically where slicing is based on profile + fix shc support + support codesystem-properties-mode + fix value set validation on profiles + fix wrong entry point on vaildating contained resources with profiles

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/validation/ValidationMessage.java

@@ -514,6 +514,7 @@ public class ValidationMessage implements Comparator<ValidationMessage>, Compara
   public String[] sliceText;
   private boolean slicingHint;
   private boolean signpost;
+  private boolean criticalSignpost;
 
 
   /**
@@ -772,9 +773,10 @@ public class ValidationMessage implements Comparator<ValidationMessage>, Compara
     return sliceHtml;
   }
 
-  public void setSliceHtml(String sliceHtml, String[] text) {
+  public ValidationMessage setSliceHtml(String sliceHtml, String[] text) {
     this.sliceHtml = sliceHtml;
     this.sliceText = text;
+    return this;
   }
 
   public String getMessageId() {
@@ -795,5 +797,14 @@ public class ValidationMessage implements Comparator<ValidationMessage>, Compara
     return this;
   }
 
+  public boolean isCriticalSignpost() {
+    return criticalSignpost;
+  }
+
+  public ValidationMessage setCriticalSignpost(boolean criticalSignpost) {
+    this.criticalSignpost = criticalSignpost;
+    return this;
+  }
+
 
 }

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

@@ -2,7 +2,11 @@ package org.hl7.fhir.validation;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.HashMap;
 
 /*
@@ -262,9 +266,9 @@ public class BaseValidator {
    * @return Returns <code>thePass</code> (in other words, returns <code>true</code> if the rule did not fail validation)
    */
   //FIXME: formatMessage should be done here
-  protected boolean slicingHint(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg, String html, String[] text) {
+  protected boolean slicingHint(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, boolean isCritical, String msg, String html, String[] text) {
     if (!thePass) {
-      addValidationMessage(errors, type, line, col, path, msg, IssueSeverity.INFORMATION, null).setSlicingHint(true).setSliceHtml(html, text);
+      addValidationMessage(errors, type, line, col, path, msg, IssueSeverity.INFORMATION, null).setSlicingHint(true).setSliceHtml(html, text).setCriticalSignpost(isCritical);
     }
     return thePass;
   }

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

@@ -139,6 +139,8 @@ public class IgLoader {
         res.cntType = Manager.FhirFormat.XML;
       else if (t.getKey().endsWith(".ttl"))
         res.cntType = Manager.FhirFormat.TURTLE;
+      else if (t.getKey().endsWith(".shc"))
+        res.cntType = Manager.FhirFormat.SHC;
       else if (t.getKey().endsWith(".txt") || t.getKey().endsWith(".map"))
         res.cntType = Manager.FhirFormat.TEXT;
       else

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

@@ -293,14 +293,10 @@ public class ValidationService {
     System.out.println((error == 0 ? "Success" : "*FAILURE*") + ": " + Integer.toString(error) + " errors, " + Integer.toString(warn) + " warnings, " + Integer.toString(info) + " notes");
     for (OperationOutcome.OperationOutcomeIssueComponent issue : oo.getIssue()) {
       System.out.println(getIssueSummary(issue));
-      if (crumbs) {
+      ValidationMessage vm = (ValidationMessage) issue.getUserData("source.msg");
-        ValidationMessage vm = (ValidationMessage) issue.getUserData("source.msg");
+      if (vm != null && vm.sliceText != null && (crumbs || vm.isCriticalSignpost())) {
-        if (vm != null) {
+        for (String s : vm.sliceText) {
-          if (vm.sliceText != null) {
+          System.out.println("    slice info: "+s);          
-            for (String s : vm.sliceText) {
-              System.out.println("    slice info: "+s);          
-            }
-          }
         }
       }
     }

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

@@ -93,6 +93,7 @@ import org.hl7.fhir.r5.model.ElementDefinition.DiscriminatorType;
 import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
 import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionConstraintComponent;
 import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionMappingComponent;
+import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionSlicingComponent;
 import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionSlicingDiscriminatorComponent;
 import org.hl7.fhir.r5.model.ElementDefinition.PropertyRepresentation;
 import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
@@ -303,7 +304,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         }
       } else if (item instanceof Element) {
         Element e = (Element) item;
-        self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL, new NodeStack(context, null, e, validationLanguage));
+        if (e.getName().equals("contained")) {
+          self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e, ctxt.getRootResource()), valerrors, e, e, sd, IdStatus.OPTIONAL, new NodeStack(context, null, e, validationLanguage));          
+        } else {
+          self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL, new NodeStack(context, null, e, validationLanguage));
+        }
       } else
         throw new NotImplementedException(context.formatMessage(I18nConstants.NOT_DONE_YET_VALIDATORHOSTSERVICESCONFORMSTOPROFILE_WHEN_ITEM_IS_NOT_AN_ELEMENT));
       boolean ok = true;
@@ -2753,7 +2758,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
               if (!isShowMessagesFromReferences()) {
                 rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, areAllBaseProfiles(profiles), I18nConstants.REFERENCE_REF_CANTMATCHCHOICE, ref, asList(type.getTargetProfile()));
                 for (StructureDefinition sd : badProfiles.keySet()) {
-                  slicingHint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false,
+                  slicingHint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, false, 
                     context.formatMessage(I18nConstants.DETAILS_FOR__MATCHING_AGAINST_PROFILE_, ref, sd.getUrl()), 
                     errorSummaryForSlicingAsHtml(badProfiles.get(sd)), errorSummaryForSlicingAsText(badProfiles.get(sd)));
                 }
@@ -2771,7 +2776,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
               if (!isShowMessagesFromReferences()) {
                 warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, I18nConstants.REFERENCE_REF_MULTIPLEMATCHES, ref, asListByUrl(goodProfiles.keySet()));
                 for (StructureDefinition sd : badProfiles.keySet()) {
-                  slicingHint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, context.formatMessage(I18nConstants.DETAILS_FOR__MATCHING_AGAINST_PROFILE_, ref, sd.getUrl()), 
+                  slicingHint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, false,  context.formatMessage(I18nConstants.DETAILS_FOR__MATCHING_AGAINST_PROFILE_, ref, sd.getUrl()), 
                       errorSummaryForSlicingAsHtml(badProfiles.get(sd)), errorSummaryForSlicingAsText(badProfiles.get(sd)));
                 }
               } else {
@@ -2898,6 +2903,15 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return "<ul>" + b.toString() + "</ul>";
   }
 
+  private boolean isCritical(List<ValidationMessage> list) {
+    for (ValidationMessage vm : list) {
+      if (vm.isSlicingHint() && vm.isCriticalSignpost()) {
+        return true;
+      }
+    }
+    return false;
+  }
+  
   private String[] errorSummaryForSlicingAsText(List<ValidationMessage> list) {
     List<String> res = new ArrayList<String>();
     for (ValidationMessage vm : list) {
@@ -3305,7 +3319,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             rr.setExternal(false);
             rr.setStack(nstack);
 //            rr.getStack().qualifyPath(".ofType("+nstack.getElement().fhirType()+")");
-            System.out.println("-->"+nstack.getLiteralPath());
+//            System.out.println("-->"+nstack.getLiteralPath());
             return rr;            
           }
           if (nstack.getElement().getSpecial() == SpecialElement.CONTAINED) {
@@ -3675,9 +3689,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     ValidatorHostContext shc = hostContext.forSlicing();
     boolean pass = evaluateSlicingExpression(shc, element, path, profile, n);
     if (!pass) {
-      slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, (context.formatMessage(I18nConstants.DOES_NOT_MATCH_SLICE_, ed.getSliceName())), "discriminator = " + Utilities.escapeXml(n.toString()), null);
+      slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, isProfile(slicer), (context.formatMessage(I18nConstants.DOES_NOT_MATCH_SLICE_, ed.getSliceName())), "discriminator = " + Utilities.escapeXml(n.toString()), null);
       for (String url : shc.getSliceRecords().keySet()) {
-        slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false,
+        slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, isProfile(slicer), 
          context.formatMessage(I18nConstants.DETAILS_FOR__MATCHING_AGAINST_PROFILE_, stack.getLiteralPath(), url),
           context.formatMessage(I18nConstants.PROFILE__DOES_NOT_MATCH_FOR__BECAUSE_OF_THE_FOLLOWING_PROFILE_ISSUES__,
               url,
@@ -3687,6 +3701,18 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return pass;
   }
 
+  private boolean isProfile(ElementDefinition slicer) {
+    if (slicer == null || !slicer.hasSlicing()) {
+      return false;
+    }
+    for (ElementDefinitionSlicingDiscriminatorComponent t : slicer.getSlicing().getDiscriminator()) {
+      if (t.getType() == DiscriminatorType.PROFILE) {
+        return true;
+      }
+    }
+    return false;
+  }
+
   public boolean evaluateSlicingExpression(ValidatorHostContext hostContext, Element element, String path, StructureDefinition profile, ExpressionNode n) throws FHIRException {
     String msg;
     boolean ok;
@@ -4898,7 +4924,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         if (ei.additionalSlice && ei.definition != null) {
           if (ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) ||
             ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPENATEND) && true /* TODO: replace "true" with condition to check that this element is at "end" */) {
-            slicingHint(errors, IssueType.INFORMATIONAL, ei.line(), ei.col(), ei.getPath(), false,
+            slicingHint(errors, IssueType.INFORMATIONAL, ei.line(), ei.col(), ei.getPath(), false, isProfile(slicer) || isCritical(ei.sliceInfo), 
               context.formatMessage(I18nConstants.THIS_ELEMENT_DOES_NOT_MATCH_ANY_KNOWN_SLICE_,
                 profile == null ? "" : " defined in the profile " + profile.getUrl()),
               context.formatMessage(I18nConstants.THIS_ELEMENT_DOES_NOT_MATCH_ANY_KNOWN_SLICE_, profile == null ? "" : I18nConstants.DEFINED_IN_THE_PROFILE + profile.getUrl()) + errorSummaryForSlicingAsHtml(ei.sliceInfo),
@@ -4944,6 +4970,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return problematicPaths;
   }
 
+
   public List<ElementInfo> listChildren(Element element, NodeStack stack) {
     // 1. List the children, and remember their exact path (convenience)
     List<ElementInfo> children = new ArrayList<ElementInfo>();
@@ -5197,7 +5224,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       }
       // todo: validate everything in this bundle.
     }
-    ok = rule(errors, IssueType.INVALID, -1, -1, stack.getLiteralPath(), typeMatchesDefn(resourceName, defn), I18nConstants.VALIDATION_VAL_PROFILE_WRONGTYPE, defn.getName(), resourceName);
+    ok = rule(errors, IssueType.INVALID, -1, -1, stack.getLiteralPath(), typeMatchesDefn(resourceName, defn), I18nConstants.VALIDATION_VAL_PROFILE_WRONGTYPE, defn.getType(), resourceName, defn.getName());
 
     if (ok) {
       if (idstatus == IdStatus.REQUIRED && (element.getNamedChild(ID) == null)) {

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

@@ -15,10 +15,12 @@ import org.hl7.fhir.convertors.factory.*;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.conformance.ProfileUtilities;
 import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
 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.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.ElementDefinition;
 import org.hl7.fhir.r5.model.ExpressionNode;
 import org.hl7.fhir.r5.model.Resource;
@@ -35,6 +37,7 @@ import org.hl7.fhir.utilities.i18n.I18nConstants;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
 import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
+import org.hl7.fhir.utilities.validation.ValidationOptions;
 import org.hl7.fhir.validation.BaseValidator;
 import org.hl7.fhir.validation.TimeTracker;
 import org.hl7.fhir.validation.instance.utils.NodeStack;
@@ -209,13 +212,23 @@ public class StructureDefinitionValidator extends BaseValidator {
       String ref = valueSet.hasPrimitiveValue() ? valueSet.primitiveValue() : valueSet.getNamedChildValue("reference");
       if (warning(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !snapshot || ref != null, I18nConstants.SD_ED_SHOULD_BIND_WITH_VS, path)) {
         Resource vs = context.fetchResource(Resource.class, ref);
-        if (warning(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs != null, I18nConstants.SD_ED_BIND_UNKNOWN_VS, path, ref)) {
+        
-          rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs instanceof ValueSet, I18nConstants.SD_ED_BIND_NOT_VS, path, ref, vs.fhirType());
+        // just because we can't resolve it directly doesn't mean that terminology server can't. Check with it
+        
+        if (warning(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs != null || serversSupportsValueSet(ref), I18nConstants.SD_ED_BIND_UNKNOWN_VS, path, ref)) {
+          if (vs != null) {
+            rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs instanceof ValueSet, I18nConstants.SD_ED_BIND_NOT_VS, path, ref, vs.fhirType());
+          }
         }
       }
     } 
   }
 
+  private boolean serversSupportsValueSet(String ref) {
+    ValidationResult vr = context.validateCode(new ValidationOptions().checkValueSetOnly().setVsAsUrl().noClient(), new Coding("http://loinc.org", "5792-7", null), new ValueSet().setUrl(ref));
+    return vr.getErrorClass() == null;
+  }
+
   private void validateElementType(List<ValidationMessage> errors, Element type, NodeStack stack, StructureDefinition sd, String path) {
     String code = type.getNamedChildValue("code");
     if (code == null && path != null) {

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

@@ -26,11 +26,20 @@ public class ValidatorHostContext {
     }
 
     public ValidatorHostContext(Object appContext, Element element) {
-        this.appContext = appContext;
+      this.appContext = appContext;
-        this.resource = element;
+      this.resource = element;
-        this.rootResource = element;
+      this.rootResource = element;
-        // no container
+      // no container
-    }
+      dump("creating");
+  }
+
+    public ValidatorHostContext(Object appContext, Element element, Element root) {
+      this.appContext = appContext;
+      this.resource = element;
+      this.rootResource = root;
+      // no container
+      dump("creating");
+  }
 
     public Object getAppContext() {
         return appContext;
@@ -52,6 +61,7 @@ public class ValidatorHostContext {
 
     public ValidatorHostContext setRootResource(Element rootResource) {
         this.rootResource = rootResource;
+        dump("setting root resource");
         return this;
     }
 
@@ -96,6 +106,7 @@ public class ValidatorHostContext {
         res.rootResource = resource;
         res.resource = element;
         res.profile = profile;
+        res.dump("forContained");
         return res;
     }
 
@@ -104,6 +115,7 @@ public class ValidatorHostContext {
         res.rootResource = element;
         res.resource = element;
         res.profile = profile;
+        res.dump("forEntry");
         return res;
     }
 
@@ -113,6 +125,7 @@ public class ValidatorHostContext {
         res.rootResource = rootResource;
         res.profile = profile;
         res.sliceRecords = sliceRecords != null ? sliceRecords : new HashMap<String, List<ValidationMessage>>();
+        res.dump("forProfile "+profile.getUrl());
         return res;
     }
 
@@ -122,15 +135,24 @@ public class ValidatorHostContext {
         res.rootResource = resource;
         res.profile = profile;
         res.checkSpecials = false;
+        res.dump("forLocalReference "+profile.getUrl());
         return res;
     }
 
+    private void dump(String ctxt) {
+//      System.out.println("** app = "+(appContext == null ? "(null)" : appContext.toString())+", res = "+resource.toString()+", root = "+rootResource.toString()+" ("+ctxt+")");
+//      if (rootResource.getName().equals("contained")) {
+//        System.out.println("** something is wrong!");        
+//      }
+    }
+
     public ValidatorHostContext forRemoteReference(StructureDefinition profile, Element resource) {
         ValidatorHostContext res = new ValidatorHostContext(appContext);
         res.resource = resource;
         res.rootResource = resource;
         res.profile = profile;
         res.checkSpecials = false;
+        res.dump("forRemoteReference "+profile.getUrl());
         return res;
     }
 
@@ -141,6 +163,7 @@ public class ValidatorHostContext {
         res.profile = profile;
         res.checkSpecials = false;
         res.sliceRecords = new HashMap<String, List<ValidationMessage>>();
+        res.dump("forSlicing");
         return res;
     }