Fix issue with comparer not rendering properly and add explicit checks around cardinality

.gitignore

@@ -304,3 +304,4 @@ local.properties
 /org.hl7.fhir.r5/src/test/resources/snapshot-generation/logical2-actual.xml
 /org.hl7.fhir.r5.new
 /org.hl7.fhir.r5.newc
+/org.hl7.fhir.r4b.new

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExamplesPackageBuilder.java

@@ -0,0 +1,74 @@
+package org.hl7.fhir.convertors.misc;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r4b.formats.JsonParser;
+import org.hl7.fhir.r4b.model.Bundle;
+import org.hl7.fhir.r4b.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.json.JsonTrackingParser;
+
+import com.google.gson.JsonArray;
+import com.google.gson.JsonObject;
+
+import org.hl7.fhir.r4b.model.SearchParameter;
+import org.hl7.fhir.r4b.utils.NPMPackageGenerator;
+import org.hl7.fhir.r4b.utils.NPMPackageGenerator.Category;
+
+public class ExamplesPackageBuilder {
+
+  public static void main(String[] args) throws FHIRFormatError, FileNotFoundException, IOException {
+    new ExamplesPackageBuilder().process(args[0]);
+
+  }
+
+  private void process(String source) throws FHIRFormatError, FileNotFoundException, IOException {
+    Set<String> set = new HashSet<>();
+    for (File f : new File(source).listFiles()) {
+      if (f.getName().endsWith(".json")) {
+        JsonObject obj = JsonTrackingParser.parseJson(new FileInputStream(f));
+        if (obj.has("resourceType") && obj.has("id")) {
+          String type = obj.get("resourceType").getAsString();
+          String id = obj.get("id").getAsString();
+          byte[] content = TextFile.fileToBytes(f);
+          if (type.equals("ConceptMap")) {
+            System.out.println("convert "+f.getName());
+            content = r5ToR4B(content);
+            TextFile.bytesToFile(content, f);
+          }
+//          TextFile.bytesToFile(content, Utilities.path(dest2, type+"-"+id+".json"));
+//          if (!set.contains(type+"/"+id)) {
+//            set.add(type+"/"+id);
+//            pck.addFile(Category.RESOURCE, type+"-"+id+".json", content);
+//          }
+        }
+      }
+    }
+//    pck.finish();
+//    
+  }
+
+  private byte[] r5ToR4B(byte[] content) throws FHIRFormatError, IOException {
+    try {
+      org.hl7.fhir.r5.model.Resource r5 = new org.hl7.fhir.r5.formats.JsonParser().parse(content);
+      org.hl7.fhir.r4.model.Resource r4 = VersionConvertorFactory_40_50.convertResource(r5);
+      return new org.hl7.fhir.r4.formats.JsonParser().composeBytes(r4);
+    } catch (Exception e) {
+      System.out.println("  .. failed: "+e.getMessage());
+      return content;
+    }
+  }
+
+}

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/engine/DefinitionsLoaderR4B.java

@@ -0,0 +1,87 @@
+package org.hl7.fhir.core.generator.engine;
+
+import java.io.IOException;
+
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r4.formats.JsonParser;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r5.model.CapabilityStatement;
+import org.hl7.fhir.r5.model.CodeSystem;
+import org.hl7.fhir.r5.model.CompartmentDefinition;
+import org.hl7.fhir.r5.model.ConceptMap;
+import org.hl7.fhir.r5.model.OperationDefinition;
+import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.SearchParameter;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.ToolsVersion;
+
+public class DefinitionsLoaderR4B {
+
+  public static Definitions load(NpmPackage npm) throws IOException {
+    Definitions res = new Definitions();
+    
+    for (String t : npm.listResources("CodeSystem")) {
+      res.getCodeSystems().see((CodeSystem) load(npm, t), null);
+    }
+    for (String t : npm.listResources("ValueSet")) {
+      res.getValuesets().see((ValueSet) load(npm, t), null);
+    }
+    for (String t : npm.listResources("ConceptMap")) {
+      res.getConceptMaps().see((ConceptMap) load(npm, t), null);
+    }
+    for (String t : npm.listResources("CapabilityStatement")) {
+      res.getStatements().see((CapabilityStatement) load(npm, t), null);
+    }
+    for (String t : npm.listResources("StructureDefinition")) {
+      res.getStructures().see((StructureDefinition) load(npm, t), null);
+    }
+    for (String t : npm.listResources("OperationDefinition")) {
+      res.getOperations().see((OperationDefinition) load(npm, t), null);
+    }
+    for (String t : npm.listResources("SearchParameter")) {
+      res.getSearchParams().see((SearchParameter) load(npm, t), null);
+    }
+    for (String t : npm.listResources("CompartmentDefinition")) {
+      res.getCompartments().see((CompartmentDefinition) load(npm, t), null);
+    }
+//    Bundle bnd = (Bundle) load(npm, "Bundle-searchParams.json");
+//    if (bnd != null) {
+//      for (BundleEntryComponent be : bnd.getEntry()) {
+//        Resource r = be.getResource();
+//        if (r instanceof CodeSystem) {
+//          res.getCodeSystems().see((CodeSystem) r, null);
+//        } else if (r instanceof ValueSet) {
+//          res.getValuesets().see((ValueSet) r, null);
+//        } else if (r instanceof ConceptMap) {
+//          res.getConceptMaps().see((ConceptMap) r, null);
+//        } else if (r instanceof CapabilityStatement) {
+//          res.getStatements().see((CapabilityStatement) r, null);
+//        } else if (r instanceof StructureDefinition) {
+//          res.getStructures().see((StructureDefinition) r, null);
+//        } else if (r instanceof OperationDefinition) {
+//          res.getOperations().see((OperationDefinition) r, null);
+//        } else if (r instanceof SearchParameter) {
+//          res.getSearchParams().see((SearchParameter) r, null);
+//        } else if (r instanceof CompartmentDefinition) {
+//          res.getCompartments().see((CompartmentDefinition) r, null);
+//        }          
+//      }
+//    }
+    return res;
+  }
+
+  public static Resource load(NpmPackage npm, String t) {
+    try {
+      return VersionConvertorFactory_40_50.convertResource(new JsonParser().parse(npm.loadResource(t)));
+    } catch (Exception e) {
+      System.out.println("Error reading "+t+": "+e.getMessage());
+      e.printStackTrace();
+      return null;
+    }
+  }
+}

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

@@ -45,14 +45,14 @@ public class ProfileComparer extends CanonicalResourceComparer {
 
   public class ProfileComparison extends CanonicalResourceComparison<StructureDefinition> {
 
-    private StructuralMatch<ElementDefinition> combined;                                             
+    private StructuralMatch<ElementDefinitionNode> combined;                                             
 
     public ProfileComparison(StructureDefinition left, StructureDefinition right) {
       super(left, right);
-      combined = new StructuralMatch<ElementDefinition>(); // base
+      combined = new StructuralMatch<ElementDefinitionNode>(); // base
     }
 
-    public StructuralMatch<ElementDefinition> getCombined() {
+    public StructuralMatch<ElementDefinitionNode> getCombined() {
       return combined;
     }
 
@@ -79,7 +79,21 @@ public class ProfileComparer extends CanonicalResourceComparer {
   }
 
 
-
+  private class ElementDefinitionNode {
+    private ElementDefinition def;
+    private StructureDefinition src;
+    private ElementDefinitionNode(StructureDefinition src, ElementDefinition def) {
+      super();
+      this.src = src;
+      this.def = def;
+    }
+    public ElementDefinition getDef() {
+      return def;
+    }
+    public StructureDefinition getSrc() {
+      return src;
+    }
+  }
 
   private ProfileUtilities utilsLeft;
   private ProfileUtilities utilsRight;
@@ -127,7 +141,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     if (left.getType().equals(right.getType())) {
       DefinitionNavigator ln = new DefinitionNavigator(session.getContextLeft(), left);
       DefinitionNavigator rn = new DefinitionNavigator(session.getContextRight(), right);
-      StructuralMatch<ElementDefinition> sm = new StructuralMatch<ElementDefinition>(ln.current(), rn.current());
+      StructuralMatch<ElementDefinitionNode> sm = new StructuralMatch<ElementDefinitionNode>(new ElementDefinitionNode(left, ln.current()), new ElementDefinitionNode(right, rn.current()));
       compareElements(res, sm, ln.path(), null, ln, rn);
       res.combined = sm;
     }
@@ -147,7 +161,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
       throw new DefinitionException("StructureDefinition snapshot is empty ("+name+": "+sd.getName()+")");
   }
 
-  private void compareElements(ProfileComparison comp, StructuralMatch<ElementDefinition> res,  String path, String sliceName, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, FHIRFormatError, IOException {
+  private void compareElements(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res,  String path, String sliceName, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, FHIRFormatError, IOException {
     assert(path != null);  
     assert(left != null);
     assert(right != null);
@@ -190,7 +204,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     subset.setExample(left.current().hasExample() ? left.current().getExample() : right.current().getExample());
 
     if (left.current().getMustSupport() != right.current().getMustSupport()) {
-      vm(IssueSeverity.ERROR, "Elements differ in definition for mustSupport:\r\n  \""+left.current().getMustSupport()+"\"\r\n  \""+right.current().getMustSupport()+"\"", path, comp.getMessages(), res.getMessages());
+      vm(IssueSeverity.WARNING, "Elements differ in definition for mustSupport:\r\n  \""+left.current().getMustSupport()+"\"\r\n  \""+right.current().getMustSupport()+"\"", path, comp.getMessages(), res.getMessages());
 
     }
     subset.setMustSupport(left.current().getMustSupport() || right.current().getMustSupport());
@@ -198,11 +212,16 @@ public class ProfileComparer extends CanonicalResourceComparer {
 
 
     // compare and intersect
-    superset.setMin(unionMin(left.current().getMin(), right.current().getMin()));
+    int leftMin = left.current().getMin();
-    superset.setMax(unionMax(left.current().getMax(), right.current().getMax()));
+    int rightMin = right.current().getMin();
-    subset.setMin(intersectMin(left.current().getMin(), right.current().getMin()));
+    int leftMax = "*".equals(left.current().getMax()) ? Integer.MAX_VALUE : Integer.parseInt(left.current().getMax());
-    subset.setMax(intersectMax(left.current().getMax(), right.current().getMax()));
+    int rightMax = "*".equals(right.current().getMax()) ? Integer.MAX_VALUE : Integer.parseInt(right.current().getMax());
-    rule(comp, res, subset.getMax().equals("*") || Integer.parseInt(subset.getMax()) >= subset.getMin(), path, "Cardinality Mismatch: "+card(left)+"/"+card(right));
+    
+    checkMinMax(comp, res, path, leftMin, rightMin, leftMax, rightMax);
+    superset.setMin(unionMin(leftMin, rightMin));
+    superset.setMax(unionMax(leftMax, rightMax, left.current().getMax(), right.current().getMax()));
+    subset.setMin(intersectMin(leftMin, rightMin));
+    subset.setMax(intersectMax(leftMax, rightMax, left.current().getMax(), right.current().getMax()));
 
     superset.getType().addAll(unionTypes(comp, res, path, left.current().getType(), right.current().getType()));
     subset.getType().addAll(intersectTypes(comp, res, subset, path, left.current().getType(), right.current().getType()));
@@ -283,7 +302,8 @@ public class ProfileComparer extends CanonicalResourceComparer {
 //    return null;
   }
 
-  private void compareChildren(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
+
+  private void compareChildren(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
     List<DefinitionNavigator> lc = left.children();
     List<DefinitionNavigator> rc = right.children();
     // it's possible that one of these profiles walks into a data type and the other doesn't
@@ -299,10 +319,10 @@ public class ProfileComparer extends CanonicalResourceComparer {
       DefinitionNavigator r = findInList(rc, l);
       if (r == null) {
         comp.getUnion().getSnapshot().getElement().add(l.current().copy());
-        res.getChildren().add(new StructuralMatch<ElementDefinition>(l.current(), vmI(IssueSeverity.INFORMATION, "Removed this element", path)));
+        res.getChildren().add(new StructuralMatch<ElementDefinitionNode>(new ElementDefinitionNode(l.getStructure(), l.current()), vmI(IssueSeverity.INFORMATION, "Removed this element", path)));
       } else {
         matchR.add(r);
-        StructuralMatch<ElementDefinition> sm = new StructuralMatch<ElementDefinition>(l.current(), r.current());
+        StructuralMatch<ElementDefinitionNode> sm = new StructuralMatch<ElementDefinitionNode>(new ElementDefinitionNode(l.getStructure(), l.current()), new ElementDefinitionNode(r.getStructure(), r.current()));
         res.getChildren().add(sm);
         compareElements(comp, sm, l.path(), null, l, r);
       }
@@ -310,7 +330,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     for (DefinitionNavigator r : rc) {
       if (!matchR.contains(r)) {
         comp.getUnion().getSnapshot().getElement().add(r.current().copy());
-        res.getChildren().add(new StructuralMatch<ElementDefinition>(vmI(IssueSeverity.INFORMATION, "Added this element", path), r.current()));        
+        res.getChildren().add(new StructuralMatch<ElementDefinitionNode>(vmI(IssueSeverity.INFORMATION, "Added this element", path), new ElementDefinitionNode(r.getStructure(), r.current())));        
       }
     }
   }
@@ -324,7 +344,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return null;
   }
 
-  private void ruleEqual(ProfileComparison comp, StructuralMatch<ElementDefinition> res, DataType vLeft, DataType vRight, String name, String path) throws IOException {
+  private void ruleEqual(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, DataType vLeft, DataType vRight, String name, String path) throws IOException {
     if (vLeft == null && vRight == null) {
       // nothing
     } else if (vLeft == null) {
@@ -356,14 +376,14 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return s;
   }
   
-  private boolean rule(ProfileComparison comp, StructuralMatch<ElementDefinition> res, boolean test, String path, String message) {
+  private boolean rule(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, boolean test, String path, String message) {
     if (!test)  {
       vm(IssueSeverity.ERROR, message, path, comp.getMessages(), res.getMessages());
     }
     return test;
   }
 
-  private String mergeText(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, String name, String left, String right, boolean isError) {
+  private String mergeText(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, String name, String left, String right, boolean isError) {
     if (left == null && right == null)
       return null;
     if (left == null)
@@ -429,6 +449,36 @@ public class ProfileComparer extends CanonicalResourceComparer {
       return right;
   }
 
+  private void checkMinMax(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, int leftMin, int rightMin, int leftMax, int rightMax) {
+    if (leftMin != rightMin) {
+      if (leftMin == 0) {
+        vm(IssueSeverity.INFORMATION, "Element minimum cardinalities differ:\r\n  \""+leftMin+"\"\r\n vs \""+rightMin+"\"", path, comp.getMessages(), res.getMessages());
+      } else if (rightMin == 0) { 
+        vm(IssueSeverity.INFORMATION, "Element minimum cardinalities differ:\r\n  \""+leftMin+"\"\r\n vs \""+rightMin+"\"", path, comp.getMessages(), res.getMessages());
+      } else {
+        vm(IssueSeverity.INFORMATION, "Element minimum cardinalities differ:\r\n  \""+leftMin+"\"\r\n vs \""+rightMin+"\"", path, comp.getMessages(), res.getMessages());
+      }
+    }    
+    if (leftMax != rightMax) {
+      if (leftMax == Integer.MAX_VALUE) {
+        vm(IssueSeverity.INFORMATION, "Element maximum cardinalities differ:\r\n  \""+leftMax+"\"\r\n vs \""+rightMax+"\"", path, comp.getMessages(), res.getMessages());
+      } else if (rightMax == Integer.MAX_VALUE) { 
+        vm(IssueSeverity.INFORMATION, "Element maximum cardinalities differ:\r\n  \""+leftMax+"\"\r\n vs \""+rightMax+"\"", path, comp.getMessages(), res.getMessages());
+      } else {
+        vm(IssueSeverity.INFORMATION, "Element maximum cardinalities differ:\r\n  \""+leftMax+"\"\r\n vs \""+rightMax+"\"", path, comp.getMessages(), res.getMessages());
+      }
+    }    
+//    rule(comp, res, subset.getMax().equals("*") || Integer.parseInt(subset.getMax()) >= subset.getMin(), path, "Cardinality Mismatch: "+card(left)+"/"+card(right));
+
+    // cross comparison - if max > min in either direction, there can be no instances that are valid against both
+    if (leftMax < rightMin) {
+      vm(IssueSeverity.ERROR, "Element minimum cardinalities conflict:\r\n  \""+leftMin+".."+leftMax+"\"\r\n vs \""+rightMin+".."+rightMax+"\": No instances can be valid against both profiles", path, comp.getMessages(), res.getMessages());      
+    }
+    if (rightMax < leftMin) {
+      vm(IssueSeverity.ERROR, "Element minimum cardinalities conflict:\r\n  \""+leftMin+".."+leftMax+"\"\r\n vs \""+rightMin+".."+rightMax+"\": No instances can be valid against both profiles", path, comp.getMessages(), res.getMessages());            
+    }
+  }
+  
   private int unionMin(int left, int right) {
     if (left > right)
       return right;
@@ -436,18 +486,14 @@ public class ProfileComparer extends CanonicalResourceComparer {
       return left;
   }
 
-  private String intersectMax(String left, String right) {
+  private String intersectMax(int l, int r, String left, String right) {
-    int l = "*".equals(left) ? Integer.MAX_VALUE : Integer.parseInt(left);
-    int r = "*".equals(right) ? Integer.MAX_VALUE : Integer.parseInt(right);
     if (l < r)
       return left;
     else
       return right;
   }
 
-  private String unionMax(String left, String right) {
+  private String unionMax(int l, int r, String left, String right) {
-    int l = "*".equals(left) ? Integer.MAX_VALUE : Integer.parseInt(left);
-    int r = "*".equals(right) ? Integer.MAX_VALUE : Integer.parseInt(right);
     if (l < r)
       return right;
     else
@@ -480,7 +526,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return Integer.toString(defn.current().getMin())+".."+defn.current().getMax();
   }
 
-  private Collection<? extends TypeRefComponent> unionTypes(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
+  private Collection<? extends TypeRefComponent> unionTypes(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
     List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
     for (TypeRefComponent l : left) 
       checkAddTypeUnion(comp, res, path, result, l, session.getContextLeft());
@@ -489,7 +535,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return result;
   }    
 
-  private void checkAddTypeUnion(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, List<TypeRefComponent> results, TypeRefComponent nw, IWorkerContext ctxt) throws DefinitionException, IOException, FHIRFormatError {
+  private void checkAddTypeUnion(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, List<TypeRefComponent> results, TypeRefComponent nw, IWorkerContext ctxt) throws DefinitionException, IOException, FHIRFormatError {
     boolean pfound = false;
     boolean tfound = false;
     nw = nw.copy();
@@ -586,7 +632,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return false;
   }
 
-  private Collection<? extends TypeRefComponent> intersectTypes(ProfileComparison comp, StructuralMatch<ElementDefinition> res, ElementDefinition ed, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
+  private Collection<? extends TypeRefComponent> intersectTypes(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, ElementDefinition ed, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
     List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
     for (TypeRefComponent l : left) {
       if (l.hasAggregation())
@@ -665,7 +711,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return b.toString();
   }
 
-  private boolean compareBindings(ProfileComparison comp, StructuralMatch<ElementDefinition> res, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) throws FHIRFormatError, DefinitionException, IOException {
+  private boolean compareBindings(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) throws FHIRFormatError, DefinitionException, IOException {
     assert(lDef.hasBinding() || rDef.hasBinding());
     if (!lDef.hasBinding()) {
       subset.setBinding(rDef.getBinding());
@@ -801,7 +847,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
   }
 
   // we can't really know about constraints. We create warnings, and collate them 
-  private List<ElementDefinitionConstraintComponent> unionConstraints(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, List<ElementDefinitionConstraintComponent> left, List<ElementDefinitionConstraintComponent> right) {
+  private List<ElementDefinitionConstraintComponent> unionConstraints(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, List<ElementDefinitionConstraintComponent> left, List<ElementDefinitionConstraintComponent> right) {
     List<ElementDefinitionConstraintComponent> result = new ArrayList<ElementDefinitionConstraintComponent>();
     for (ElementDefinitionConstraintComponent l : left) {
       boolean found = false;
@@ -829,7 +875,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return result;
   }
 
-  private StructureDefinition resolveProfile(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, String url, String name, IWorkerContext ctxt) {
+  private StructureDefinition resolveProfile(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, String url, String name, IWorkerContext ctxt) {
     StructureDefinition sd = ctxt.fetchResource(StructureDefinition.class, url);
     if (sd == null) {
       ValidationMessage vm = vmI(IssueSeverity.WARNING, "Unable to resolve profile "+url+" in profile "+name, path);
@@ -841,7 +887,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return binding.getStrength() == BindingStrength.EXAMPLE || binding.getStrength() == BindingStrength.PREFERRED;
   }
 
-  private ElementDefinitionBindingComponent unionBindings(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, ElementDefinitionBindingComponent left, ElementDefinitionBindingComponent right) throws FHIRFormatError, DefinitionException, IOException {
+  private ElementDefinitionBindingComponent unionBindings(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, ElementDefinitionBindingComponent left, ElementDefinitionBindingComponent right) throws FHIRFormatError, DefinitionException, IOException {
     ElementDefinitionBindingComponent union = new ElementDefinitionBindingComponent();
     if (left.getStrength().compareTo(right.getStrength()) < 0)
       union.setStrength(left.getStrength());
@@ -881,17 +927,17 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return gen.generate(model, prefix, 0, null);
   }
 
-  private void genElementComp(String defPath, HierarchicalTableGenerator gen, List<Row> rows, StructuralMatch<ElementDefinition> combined, String corePath, String prefix, Row slicingRow, boolean root) throws IOException {
+  private void genElementComp(String defPath, HierarchicalTableGenerator gen, List<Row> rows, StructuralMatch<ElementDefinitionNode> combined, String corePath, String prefix, Row slicingRow, boolean root) throws IOException {
     Row originalRow = slicingRow;
     Row typesRow = null;
     
-    List<StructuralMatch<ElementDefinition>> children = combined.getChildren();
+    List<StructuralMatch<ElementDefinitionNode>> children = combined.getChildren();
 
     Row row = gen.new Row();
     rows.add(row);
-    String path = combined.either().getPath();
+    String path = combined.either().getDef().getPath();
     row.setAnchor(path);
-      row.setColor(utilsRight.getRowColor(combined.either(), false));
+      row.setColor(utilsRight.getRowColor(combined.either().getDef(), false));
       if (eitherHasSlicing(combined))
         row.setLineColor(1);
       else if (eitherHasSliceName(combined))
@@ -917,7 +963,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
           row.setIcon("icon_choice.gif", HierarchicalTableGenerator.TEXT_ICON_CHOICE);
           typesRow = row;
         }
-      } else if (combined.either().hasContentReference())
+      } else if (combined.either().getDef().hasContentReference())
         row.setIcon("icon_reuse.png", HierarchicalTableGenerator.TEXT_ICON_REUSE);
       else if (isPrimitive(combined))
         row.setIcon("icon_primitive.png", HierarchicalTableGenerator.TEXT_ICON_PRIMITIVE);
@@ -927,7 +973,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
         row.setIcon("icon_datatype.gif", HierarchicalTableGenerator.TEXT_ICON_DATATYPE);
       else
         row.setIcon("icon_resource.png", HierarchicalTableGenerator.TEXT_ICON_RESOURCE);
-      String ref = defPath == null ? null : defPath + combined.either().getId();
+      String ref = defPath == null ? null : defPath + combined.either().getDef().getId();
       String sName = tail(path);
       String sn = getSliceName(combined);
       if (sn != null)
@@ -937,23 +983,23 @@ public class ProfileComparer extends CanonicalResourceComparer {
       String leftColor = !combined.hasLeft() ? COLOR_NO_ROW_LEFT : combined.hasErrors() ? COLOR_DIFFERENT : null;
       String rightColor = !combined.hasRight() ? COLOR_NO_ROW_LEFT : combined.hasErrors() ? COLOR_DIFFERENT : null;
       if (combined.hasLeft()) {
-        nc = utilsRight.genElementNameCell(gen, combined.getLeft(),  "??", true, corePath, prefix, root, false, false, null, typesRow, row, false, ext, used , ref, sName);
+        nc = utilsRight.genElementNameCell(gen, combined.getLeft().getDef(),  "??", true, corePath, prefix, root, false, false, combined.getLeft().getSrc(), typesRow, row, false, ext, used , ref, sName);
       } else {
-        nc = utilsRight.genElementNameCell(gen, combined.getRight(),  "??", true, corePath, prefix, root, false, false, null, typesRow, row, false, ext, used , ref, sName);
+        nc = utilsRight.genElementNameCell(gen, combined.getRight().getDef(),  "??", true, corePath, prefix, root, false, false, combined.getRight().getSrc(), typesRow, row, false, ext, used , ref, sName);
       }
       if (combined.hasLeft()) {
-        frame(utilsRight.genElementCells(gen, combined.getLeft(),  "??", true, corePath, prefix, root, false, false, null, typesRow, row, false, ext, used , ref, sName, nc, false), leftColor);
+        frame(utilsRight.genElementCells(gen, combined.getLeft().getDef(),  "??", true, corePath, prefix, root, false, false, combined.getLeft().getSrc(), typesRow, row, true, ext, used , ref, sName, nc, false), leftColor);
       } else {
         frame(spacers(row, 4, gen), leftColor);
       }
       if (combined.hasRight()) {
-        frame(utilsRight.genElementCells(gen, combined.getRight(), "??", true, corePath, prefix, root, false, false, null, typesRow, row, false, ext, used, ref, sName, nc, false), rightColor);
+        frame(utilsRight.genElementCells(gen, combined.getRight().getDef(), "??", true, corePath, prefix, root, false, false, combined.getRight().getSrc(), typesRow, row, true, ext, used, ref, sName, nc, false), rightColor);
       } else {
         frame(spacers(row, 4, gen), rightColor);
       }
       row.getCells().add(cellForMessages(gen, combined.getMessages()));
 
-      for (StructuralMatch<ElementDefinition> child : children) {
+      for (StructuralMatch<ElementDefinitionNode> child : children) {
         genElementComp(defPath, gen, row.getSubRows(), child, corePath, prefix, originalRow, false);
       }
     }
@@ -978,47 +1024,47 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return res;
   }
 
-  private String getSliceName(StructuralMatch<ElementDefinition> combined) {
+  private String getSliceName(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub
     return null;
   }
 
-  private boolean isDataType(StructuralMatch<ElementDefinition> combined) {
+  private boolean isDataType(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub
     return false;
   }
 
-  private boolean hasTarget(StructuralMatch<ElementDefinition> combined) {
+  private boolean hasTarget(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub
     return false;
   }
 
-  private boolean isPrimitive(StructuralMatch<ElementDefinition> combined) {
+  private boolean isPrimitive(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub
     return false;
   }
 
-  private boolean allAreReference(StructuralMatch<ElementDefinition> combined) {
+  private boolean allAreReference(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub
     return false;
   }
 
-  private boolean hasChoice(StructuralMatch<ElementDefinition> combined) {
+  private boolean hasChoice(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub
     return false;
   }
 
-  private boolean elementIsComplex(StructuralMatch<ElementDefinition> combined) {
+  private boolean elementIsComplex(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub velement.hasType() && element.getType().get(0).hasProfile() && extensionIsComplex(element.getType().get(0).getProfile().get(0).getValue()
     return false;
   }
 
-  private boolean eitherHasSliceName(StructuralMatch<ElementDefinition> combined) {
+  private boolean eitherHasSliceName(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub
     return false;
   }
 
-  private boolean eitherHasSlicing(StructuralMatch<ElementDefinition> combined) {
+  private boolean eitherHasSlicing(StructuralMatch<ElementDefinitionNode> combined) {
     // TODO Auto-generated method stub
     return false;
   }

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

@@ -301,11 +301,11 @@ public class ResourceComparer {
   private String halfColorForLevel(IssueSeverity level) {
     switch (level) {
     case ERROR:
-      return "#ffeeee";
+      return "#ffdddd";
     case FATAL:
       return "#ffcccc";
     case WARNING:
-      return "#fff4ee";
+      return "#fff6ee";
     default: // INFORMATION:
       return "#fffff2";
     }
@@ -319,6 +319,9 @@ public class ResourceComparer {
       XhtmlNode li = new XhtmlNode(NodeType.Element, "li");
       piece.getChildren().add(li);
       li.style("background-color: "+halfColorForLevel(msg.getLevel()));
+      if (msg.getLevel() == IssueSeverity.ERROR) {
+        li.style("font-weight: bold");
+      }
       li.tx(msg.getMessage());
     }
     return cell;

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

@@ -4,6 +4,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.hl7.fhir.r5.comparison.ResourceComparer.MessageCounts;
+import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
@@ -114,4 +115,5 @@ public class StructuralMatch<T> {
   }
 
 
+  
 }

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

@@ -36,6 +36,9 @@ import java.io.FileReader;
 
 import java.io.IOException;
 import java.io.OutputStream;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
@@ -3504,7 +3507,7 @@ public class ProfileUtilities extends TranslatingUtilities {
     List<TypeRefComponent> types = e.getType();
     if (!e.hasType()) {
       if (root) { // we'll use base instead of types then
-        StructureDefinition bsd = context.fetchResource(StructureDefinition.class, profile.getBaseDefinition());
+        StructureDefinition bsd = profile == null ? null : context.fetchResource(StructureDefinition.class, profile.getBaseDefinition());
         if (bsd != null) {
           if (bsd.hasUserData("path")) {
             c.getPieces().add(gen.new Piece(Utilities.isAbsoluteUrl(bsd.getUserString("path")) ? bsd.getUserString("path") : imagePath +bsd.getUserString("path"), bsd.getName(), null));
@@ -3586,7 +3589,7 @@ public class ProfileUtilities extends TranslatingUtilities {
                 c.addPiece(checkForNoChange(tl, gen.new Piece(null,", ", null)));
               }          
 
-              ref = pkp.getLinkForProfile(profile, p.getValue());
+              ref = pkp == null ? null : pkp.getLinkForProfile(profile, p.getValue());
               if (ref != null) {
                 String[] parts = ref.split("\\|");
                 if (parts[0].startsWith("http:") || parts[0].startsWith("https:")) {
@@ -3685,7 +3688,7 @@ public class ProfileUtilities extends TranslatingUtilities {
 
 
   private String checkPrepend(String corePath, String path) {
-    if (pkp.prependLinks() && !(path.startsWith("http:") || path.startsWith("https:")))
+    if (pkp != null && pkp.prependLinks() && !(path.startsWith("http:") || path.startsWith("https:")))
       return corePath+path;
     else 
       return path;
@@ -4566,7 +4569,7 @@ public class ProfileUtilities extends TranslatingUtilities {
         }
       }
       if (root) {
-        if (profile.getAbstract()) {
+        if (profile != null && profile.getAbstract()) {
           if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
           c.addPiece(gen.new Piece(null, "This is an abstract profile", null));          
         }
@@ -4661,7 +4664,7 @@ public class ProfileUtilities extends TranslatingUtilities {
           if (binding!=null && !binding.isEmpty()) {
             if (!c.getPieces().isEmpty()) 
               c.addPiece(gen.new Piece("br"));
-            BindingResolution br = pkp.resolveBinding(profile, binding, definition.getPath());
+            BindingResolution br = pkp == null ? makeNullBr(binding) : pkp.resolveBinding(profile, binding, definition.getPath());
             c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, translate("sd.table", "Binding")+": ", null).addStyle("font-weight:bold")));
               c.getPieces().add(checkForNoChange(binding.getValueSetElement(), gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath+br.url, br.display, null)));
             if (binding.hasStrength()) {
@@ -4670,7 +4673,7 @@ public class ProfileUtilities extends TranslatingUtilities {
               c.getPieces().add(checkForNoChange(binding.getStrengthElement(), gen.new Piece(null, ")", null)));
             }
             if (binding.hasExtension(ToolingExtensions.EXT_MAX_VALUESET)) {
-              br = pkp.resolveBinding(profile, ToolingExtensions.readStringExtension(binding, ToolingExtensions.EXT_MAX_VALUESET), definition.getPath());
+              br = pkp == null ? makeNullBr(binding) : pkp.resolveBinding(profile, ToolingExtensions.readStringExtension(binding, ToolingExtensions.EXT_MAX_VALUESET), definition.getPath());
               c.addPiece(gen.new Piece("br"));
               c.getPieces().add(checkForNoChange(binding, gen.new Piece(corePath+"extension-elementdefinition-maxvalueset.html", translate("sd.table", "Max Binding")+": ", "Max 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)));
@@ -4764,6 +4767,13 @@ public class ProfileUtilities extends TranslatingUtilities {
     return c;
   }
 
+  private BindingResolution makeNullBr(ElementDefinitionBindingComponent binding) {
+    BindingResolution br = new BindingResolution();
+    br.url = "http://none.none/none";
+    br.display = "todo";
+    return br;
+  }
+
   private ElementDefinitionBindingComponent makeUnifiedBinding(ElementDefinitionBindingComponent binding, ElementDefinition element) {
     if (!element.hasUserData(DERIVATION_POINTER)) {
       return binding;

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

@@ -614,6 +614,9 @@ public class ExpressionNode {
 
 	public String check() {
 
+	  if (kind == null) {
+	    return "Error in expression - node has no kind";
+	  }
 		switch (kind) {
 		case Name:
 			if (Utilities.noString(name)) 

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

@@ -511,7 +511,7 @@ public class ToolingExtensions {
    * @return The extension, if on this element, else null
    */
   public static Extension getExtension(DomainResource resource, String name) {
-    if (name == null)
+    if (resource == null || name == null)
       return null;
     if (!resource.hasExtension())
       return null;