fixes to snapshot generation and validation for Bundle.tnry slicing by resource profile

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

@@ -248,6 +248,8 @@ public class ProfileUtilities extends TranslatingUtilities {
   public static final String IS_DERIVED = "derived.fact";
   public static final String UD_ERROR_STATUS = "error-status";
   private static final String GENERATED_IN_SNAPSHOT = "profileutilities.snapshot.processed";
+  private static final boolean COPY_BINDING_EXTENSIONS = false;
+  private static final boolean DONT_DO_THIS = false;
   private final boolean ADD_REFERENCE_TO_TABLE = true;
 
   private boolean useTableForFixedValues = true;
@@ -574,6 +576,34 @@ public class ProfileUtilities extends TranslatingUtilities {
           }
         }
       }
+      // last, check for wrong profiles or target profiles 
+      for (ElementDefinition ed : derived.getSnapshot().getElement()) {
+        for (TypeRefComponent t : ed.getType()) {
+          for (UriType u : t.getProfile()) {
+            StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
+            if (sd == null) {
+              if (messages != null) {
+                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), "The type of profile "+u.getValue()+" cannot be checked as the profile is not known", IssueSeverity.WARNING));
+              }
+            } else {
+              String wt = t.getWorkingCode();
+              if (ed.getPath().equals("Bundle.entry.response.outcome")) {
+                wt = "OperationOutcome";
+              }
+              if (!sd.getType().equals(wt)) {
+                boolean ok = isCompatibleType(wt, sd.getType());
+                if (!ok) {
+                  String smsg = "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt;
+                  if (exception)
+                    throw new DefinitionException(smsg);
+                  else
+                    messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), smsg, IssueSeverity.ERROR));
+                }
+              }
+            }
+          }
+        }
+      }
     } catch (Exception e) {
       // if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
       derived.setSnapshot(null);
@@ -581,6 +611,18 @@ public class ProfileUtilities extends TranslatingUtilities {
     }
   }
 
+  private boolean isCompatibleType(String base, String type) {
+    StructureDefinition sd = context.fetchTypeDefinition(type);
+    while (sd != null) {
+      if (sd.getType().equals(base)) {
+        return true;
+      }
+      sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition()); 
+    }
+    return false;
+  }
+
+
   private StructureDefinitionDifferentialComponent cloneDiff(StructureDefinitionDifferentialComponent source) {
     StructureDefinitionDifferentialComponent diff = new StructureDefinitionDifferentialComponent();
     for (ElementDefinition sed : source.getElement()) {
@@ -2293,10 +2335,25 @@ public class ProfileUtilities extends TranslatingUtilities {
                 messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, pn+"."+derived.getPath(), "Unable to check if "+derived.getBinding().getValueSet()+" is a proper subset of " +base.getBinding().getValueSet()+" - base value set is too large to check", ValidationMessage.IssueSeverity.WARNING));
               else if (!isSubset(expBase.getValueset(), expDerived.getValueset()))
                 messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, pn+"."+derived.getPath(), "Binding "+derived.getBinding().getValueSet()+" is not a subset of binding "+base.getBinding().getValueSet(), ValidationMessage.IssueSeverity.ERROR));
-
             }
           }
-          base.setBinding(derived.getBinding().copy());
+          ElementDefinitionBindingComponent d = derived.getBinding();
+          ElementDefinitionBindingComponent nb = base.getBinding().copy();
+          if (!COPY_BINDING_EXTENSIONS) {
+            nb.getExtension().clear();
+          }
+          nb.setDescription(null);
+          nb.getExtension().addAll(d.getExtension());
+          if (d.hasStrength()) {
+            nb.setStrength(d.getStrength());
+          }
+          if (d.hasDescription()) {
+            nb.setDescription(d.getDescription());
+          }
+          if (d.hasValueSet()) {
+            nb.setValueSet(d.getValueSet());
+          }
+          base.setBinding(nb);
         } else if (trimDifferential)
           derived.setBinding(null);
         else
@@ -2316,31 +2373,61 @@ public class ProfileUtilities extends TranslatingUtilities {
       }
 
       if (derived.hasType()) {
-//        if (derived.getPath().endsWith("[x]") && derived.hasSlicing() && derived.getSlicing().getRules() != SlicingRules.CLOSED) {
+        if (!Base.compareDeep(derived.getType(), base.getType(), false)) {
-//          // if we're slicing, and not closed, then it's the same list
-//
-//          derived.getType().clear();
-//          derived.getType().addAll(base.getType());
-//        } else
-          if (!Base.compareDeep(derived.getType(), base.getType(), false)) {
           if (base.hasType()) {
             for (TypeRefComponent ts : derived.getType()) {
-//              if (!ts.hasCode()) { // ommitted in the differential; copy it over....
-//                if (base.getType().size() > 1) 
-//                  throw new DefinitionException("StructureDefinition "+pn+" at "+derived.getPath()+": constrained type code must be present if there are multiple types ("+base.typeSummary()+")");
-//                if (base.getType().get(0).getCode() != null)
-//                  ts.setCode(base.getType().get(0).getCode());
-//              }
               boolean ok = false;
               CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
               String t = ts.getWorkingCode();
               for (TypeRefComponent td : base.getType()) {;
                 String tt = td.getWorkingCode();
                 b.append(tt);
-                if (td.hasCode() && (tt.equals(t) || "Extension".equals(tt) || (t.equals("uri") && tt.equals("string"))  || // work around for old badly generated SDs
+                if (td.hasCode() && (tt.equals(t))) {
-                    "Element".equals(tt) || "*".equals(tt) ||
-                    (("Resource".equals(tt) || ("DomainResource".equals(tt)) && pkp.isResource(t)))))
                   ok = true;
+                }
+                if (!ok) {
+                  StructureDefinition sdt = context.fetchTypeDefinition(tt);
+                  if (sdt != null && sdt.getAbstract()) {
+                    StructureDefinition sdb = context.fetchTypeDefinition(t);
+                    while (sdb != null && !ok) {
+                      ok = sdb.getType().equals(sdt.getUrl());
+                      sdb = context.fetchResource(StructureDefinition.class, sdb.getBaseDefinition());
+                    }
+                  }
+                }
+               // work around for old badly generated SDs
+                if (DONT_DO_THIS && Utilities.existsInList(tt, "Extension", "uri", "string", "Element")) {
+                  ok = true;
+                }
+                if (DONT_DO_THIS && Utilities.existsInList(tt, "Resource","DomainResource") && pkp.isResource(t)) {
+                  ok = true;
+                }
+                if (ok && ts.hasTargetProfile()) {
+                  // check that any derived target has a reference chain back to one of the base target profiles 
+                  for (UriType u : ts.getTargetProfile()) {
+                    boolean tgtOk = false;
+                    String url = u.getValue();
+                    while (url != null && !td.hasTargetProfile(url)) {
+                      StructureDefinition sd = context.fetchResource(StructureDefinition.class, url);
+                      if (sd == null) {
+                        if (messages != null) {
+                          messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, purl+"#"+derived.getPath(), "Connect check whether the target profile "+url+" is valid constraint on the base because it is not known", IssueSeverity.WARNING));
+                        }
+                        url = null;
+                        tgtOk = true; // suppress error message
+                      } else {
+                        url = sd.getBaseDefinition();
+                      }
+                    }
+                    if (!tgtOk) {
+                      if (messages == null) {
+                        throw new FHIRException("Error at "+purl+"#"+derived.getPath()+": The target profile "+url+" is not  valid constraint on the base ("+td.getTargetProfile()+")");
+                      } else {
+                        messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, pn+"."+derived.getPath(), "The target profile "+url+" is not  valid constraint on the base ("+td.getTargetProfile()+")", IssueSeverity.ERROR));
+                      }
+                    }
+                  }
+                }
               }
               if (!ok)
                 throw new DefinitionException("StructureDefinition "+purl+" at "+derived.getPath()+": illegal constrained type "+t+" from "+b.toString()+" in "+srcSD.getUrl());

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java

@@ -4287,19 +4287,73 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
 
   private void validateContains(ValidatorHostContext hostContext, List<ValidationMessage> errors, String path, ElementDefinition child, ElementDefinition context, Element resource, Element element, NodeStack stack, IdStatus idstatus) throws FHIRException, FHIRException, IOException {
     String resourceName = element.getType();
-    long t = System.nanoTime();
+    TypeRefComponent trr = null;
-    StructureDefinition profile = this.context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName);
+    for (TypeRefComponent tr : child.getType()) {
-    sdTime = sdTime + (System.nanoTime() - t);
+      if (tr.getCode().equals("Resource")) {
-    // special case: resource wrapper is reset if we're crossing a bundle boundary, but not otherwise
+        trr = tr;
-    ValidatorHostContext hc = null;
+        break;
-    if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY || element.getSpecial() == SpecialElement.BUNDLE_OUTCOME || element.getSpecial() == SpecialElement.PARAMETER ) {
+      }
-      resource = element;
-      hc = hostContext.forEntry(element);
-    } else {
-      hc = hostContext.forContained(element);
     }
-    if (rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), profile != null, "No profile found for contained resource of type '" + resourceName + "'"))
+    if (trr == null) {
-      validateResource(hc, errors, resource, element, profile, null, idstatus, stack, false);
+      rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '"+resourceName+" is not valid - no resources allowed here");
+    } else if (isValidResourceType(resourceName, trr)) {
+      long t = System.nanoTime();
+      StructureDefinition profile = this.context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName);
+      sdTime = sdTime + (System.nanoTime() - t);
+      // special case: resource wrapper is reset if we're crossing a bundle boundary, but not otherwise
+      ValidatorHostContext hc = null;
+      if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY || element.getSpecial() == SpecialElement.BUNDLE_OUTCOME || element.getSpecial() == SpecialElement.PARAMETER ) {
+        resource = element;
+        hc = hostContext.forEntry(element);
+      } else {
+        hc = hostContext.forContained(element);
+      }
+      if (rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), profile != null, "No profile found for contained resource of type '" + resourceName + "'")) {
+        validateResource(hc, errors, resource, element, profile, null, idstatus, stack, false);
+      }
+    } else {
+      List<String> types = new ArrayList<>();
+      for (UriType u : trr.getProfile()) {
+        StructureDefinition sd = this.context.fetchResource(StructureDefinition.class, u.getValue());
+        if (sd != null && !types.contains(sd.getType())) {
+          types.add(sd.getType());
+        }
+      }
+      if (types.size() == 1) {
+        rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '"+resourceName+"' is not valid - must be "+types.get(0));
+      } else {
+          rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '"+resourceName+"' is not valid - must be one of "+types);
+      }
+    }
+  }
+
+  private boolean isValidResourceType(String type, TypeRefComponent def) {
+    if (!def.hasProfile()) {
+      return true;
+    }
+    List<StructureDefinition> list = new ArrayList<>();
+    for (UriType u : def.getProfile()) {
+      StructureDefinition sdt = context.fetchResource(StructureDefinition.class, u.getValue());
+      if (sdt != null) {
+        list.add(sdt);
+      }
+    }
+    
+    StructureDefinition sdt = context.fetchTypeDefinition(type);
+    while (sdt != null) {
+      if (def.getWorkingCode().equals("Resource")) {
+        for (StructureDefinition sd : list) {
+          if (sd.getUrl().equals(sdt.getUrl())) {
+            return true;
+          }
+          if (sd.getType().equals(sdt.getType())) {
+            return true;
+          }
+        }
+      }
+      sdt = context.fetchResource(StructureDefinition.class, sdt.getBaseDefinition());
+    }
+    return false;
   }
 
   private void validateDocument(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id) {
@@ -4480,6 +4534,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
       checkInvariants(hostContext, errors, profile, ei.definition, resource, ei.element, localStack, true);
 
       ei.element.markValidation(profile, ei.definition);
+      boolean elementValidated = false;
       if (type != null) {
         if (isPrimitiveType(type)) {
           checkPrimitive(hostContext, errors, ei.path, type, ei.definition, ei.element, profile, stack);
@@ -4514,6 +4569,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
           }
         } else if (type.equals("Resource")) {
           validateContains(hostContext, errors, ei.path, ei.definition, definition, resource, ei.element, localStack, idStatusForEntry(element, ei)); // if
+          elementValidated = true;
         // (str.matches(".*([.,/])work\\1$"))
         } else if (Utilities.isAbsoluteUrl(type)) {
           StructureDefinition defn = context.fetchTypeDefinition(type);
@@ -4532,7 +4588,6 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
           validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.element, type, localStack, false, true, null);
       }
       StructureDefinition p = null;
-      boolean elementValidated = false;
       String tail = null;
       if (profiles.isEmpty()) {
         if (type != null) {