Merge pull request #872 from hapifhir/gg-202207-bug-fixes

Gg 202207 bug fixes

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

@@ -4229,6 +4229,7 @@ public class ProfileUtilities extends TranslatingUtilities {
         Row currRow = row;
         List<ElementChoiceGroup> groups = readChoices(element, children);
         boolean isExtension = Utilities.existsInList(tail(element.getPath()), "extension", "modifierExtension");
+        if (!element.prohibited()) {
           for (ElementDefinition child : children) {
             if (!child.hasSliceName()) {
               currRow = row; 
@@ -4239,6 +4240,7 @@ public class ProfileUtilities extends TranslatingUtilities {
               currRow = genElement(defPath, gen, childRow.getSubRows(), child, all, profiles, showMissing, profileBaseFileName, isExtension, snapshot, corePath, imagePath, false, logicalModel, isConstraintMode, allInvariants, currRow, mustSupport, rc);
             }
           }
+        }
 //        if (!snapshot && (extensions == null || !extensions))
 //          for (ElementDefinition child : children)
 //            if (child.getPath().endsWith(".extension") || child.getPath().endsWith(".modifierExtension"))
@@ -4349,7 +4351,7 @@ public class ProfileUtilities extends TranslatingUtilities {
           res.add(addCell(row, gen.new Cell(null, null, "?gen-e1? "+element.getType().get(0).getProfile(), null, null)));
           res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, profile == null ? "" : profile.getUrl(), eurl, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport, allowSubRows, rc));
         } else {
-          String name = urltail(eurl);
+          String name = element.hasSliceName() ? element.getSliceName() : urltail(eurl);
           nameCell.getPieces().get(0).setText(name);
           // left.getPieces().get(0).setReference((String) extDefn.getExtensionStructure().getTag("filename"));
           nameCell.getPieces().get(0).setHint(translate("sd.table", "Extension URL")+" = "+extDefn.getUrl());

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/R5ExtensionsLoader.java

@@ -45,6 +45,7 @@ public class R5ExtensionsLoader {
     JsonParser json = new JsonParser();
     for (PackageResourceInformation pri : pck.listIndexedResources(types)) {
       CanonicalResource r = (CanonicalResource) json.parse(pck.load(pri));
+      r.setUserData("path", Utilities.pathURL(pck.getWebLocation(), r.fhirType().toLowerCase()+ "-"+r.getId().toLowerCase()+".html"));
       if (r instanceof CodeSystem) {
         codeSystems.put(r.getUrl(), (CodeSystem) r);
       } else if (r instanceof ValueSet) {
@@ -75,7 +76,7 @@ public class R5ExtensionsLoader {
     for (ElementDefinition ed : sd.getSnapshot().getElement()) {
       if (ed.hasBinding() && ed.getBinding().hasValueSet()) {
         String vs = ed.getBinding().getValueSet();
-        if (!context.hasResource(StructureDefinition.class, vs)) {
+        if (!context.hasResource(ValueSet.class, vs)) {
           loadValueSet(vs, context, valueSets, codeSystems, pd);
         }
       }

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

@@ -55,8 +55,8 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.utilities.ElementDecoration;
 import org.hl7.fhir.utilities.ElementDecoration.DecorationType;
-import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 
 /**
@@ -360,9 +360,12 @@ public class Element extends Base {
     if (childMap == null) {
       childMap = new HashMap<>();
       for (Element child : children) {
-        String n = child.getName();
+        String n;
-        if (n.endsWith("[x]")) {
+        if (child.getProperty().getName().endsWith("[x]")) {
+          n = child.getProperty().getName();
           n = n.substring(0, n.length()-3);
+        } else {
+          n = child.getName();
         }
         List<Element> l = childMap.get(n);
         if (l == null) {

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

@@ -54,8 +54,8 @@ import org.hl7.fhir.r5.formats.JsonCreator;
 import org.hl7.fhir.r5.formats.JsonCreatorCanonical;
 import org.hl7.fhir.r5.formats.JsonCreatorGson;
 import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
-import org.hl7.fhir.r5.utils.FHIRPathEngine;
 import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.utils.FHIRPathEngine;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
@@ -477,6 +477,7 @@ public class JsonParser extends ParserBase {
   }
 
   private void compose(String path, Element e, Set<String> done, Element child) throws IOException {
+    if (wantCompose(path, child)) {
       boolean isList = child.hasElementProperty() ? child.getElementProperty().isList() : child.getProperty().isList();
       if (!isList) {// for specials, ignore the cardinality of the stated type
         compose(path, child);
@@ -486,6 +487,8 @@ public class JsonParser extends ParserBase {
         composeList(path, list);
       }
     }
+  }
+
 
   private void composeList(String path, List<Element> list) throws IOException {
     // there will be at least one element

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

@@ -40,7 +40,6 @@ import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.context.IWorkerContext;
-import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
 import org.hl7.fhir.r5.formats.FormatUtilities;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.model.StructureDefinition;
@@ -55,6 +54,18 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
 
 public abstract class ParserBase {
 
+  public enum IdRenderingPolicy {
+    All, None, RootOnly, NotRoot;
+
+    boolean forRoot() {
+      return this == All || this == RootOnly;
+    }
+
+    boolean forInner() {
+      return this == All || this == NotRoot;
+    }
+  }
+
   public class NamedElement {
     private String name;
     private Element element;
@@ -92,6 +103,7 @@ public abstract class ParserBase {
   protected List<ValidationMessage> errors;
   protected ILinkResolver linkResolver;
   protected boolean showDecorations;
+  protected IdRenderingPolicy idPolicy = IdRenderingPolicy.All;
   
 	public ParserBase(IWorkerContext context) {
 		super();
@@ -194,4 +206,23 @@ public abstract class ParserBase {
   }
 
 
+  public IdRenderingPolicy getIdPolicy() {
+    return idPolicy;
+  }
+
+  public void setIdPolicy(IdRenderingPolicy idPolicy) {
+    this.idPolicy = idPolicy;
+  }
+
+  protected boolean wantCompose(String path, Element e) {
+    if (!"id".equals(e.getName())) {
+      return true;
+    }
+    if (path.contains(".")) {
+      return idPolicy.forInner();
+    } else {
+      return idPolicy.forRoot();
+    }
+  }
+
 }

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

@@ -13,7 +13,6 @@ import java.util.Map.Entry;
 import java.util.zip.DataFormatException;
 import java.util.zip.Inflater;
 
-import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
@@ -22,15 +21,14 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
-import org.hl7.fhir.utilities.json.JsonUtilities;
 import org.hl7.fhir.utilities.json.JsonTrackingParser;
 import org.hl7.fhir.utilities.json.JsonTrackingParser.LocationData;
+import org.hl7.fhir.utilities.json.JsonUtilities;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
 
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
-import com.google.gson.JsonNull;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonPrimitive;
 

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

@@ -34,13 +34,11 @@ package org.hl7.fhir.r5.elementmodel;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
-import java.util.List;
 import java.util.Map.Entry;
 
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
-import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;

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

@@ -43,7 +43,6 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
-import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
 import org.hl7.fhir.r5.model.StructureDefinition;
@@ -395,6 +394,10 @@ public class TurtleParser extends ParserBase {
 //            (element.getProperty().getDefinition().getIsModifier()? "modifierExtension" : "extension") ; 
     String en = getFormalName(element);
 
+    if (!wantCompose(parent == null ? "" : parent.getPath(), element)) {
+      return;
+    }
+    
 	  Complex t;
 	  if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY && parent != null && parent.getNamedChildValue("fullUrl") != null) {
 	    String url = "<"+parent.getNamedChildValue("fullUrl")+">";

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

@@ -43,7 +43,6 @@ import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.context.IWorkerContext;
-import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.model.StructureDefinition;
 

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

@@ -53,7 +53,6 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.conformance.ProfileUtilities;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
-import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
 import org.hl7.fhir.r5.formats.FormatUtilities;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.model.DateTimeType;
@@ -702,7 +701,7 @@ public class XmlParser extends ParserBase {
     } else {
       setXsiTypeIfIsTypeAttr(xml, element);
       for (Element child : element.getChildren()) {
-        if (isAttr(child.getProperty())) {
+        if (isAttr(child.getProperty()) && wantCompose(element.getPath(), child)) {
           if (linkResolver != null)
             xml.link(linkResolver.resolveType(child.getType()));
           String av = child.getValue();
@@ -720,12 +719,14 @@ public class XmlParser extends ParserBase {
         xml.enter(element.getProperty().getXmlNamespace(),element.getType());
       }
       for (Element child : element.getChildren()) {
+        if (wantCompose(element.getPath(), child)) {
           if (isText(child.getProperty())) {
             if (linkResolver != null)
               xml.link(linkResolver.resolveProperty(element.getProperty()));
             xml.text(child.getValue());
           } else if (!isAttr(child.getProperty()))
             composeElement(xml, child, child.getName(), false);
+        }
       }
 	    if (!root && element.getSpecial() != null)
         xml.exit(element.getProperty().getXmlNamespace(),element.getType());

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/BundleRenderer.java

@@ -167,6 +167,9 @@ public class BundleRenderer extends ResourceRenderer {
   }
 
   private ResourceWrapper resolveReference(List<BaseWrapper> entries, Base base) throws UnsupportedEncodingException, FHIRException, IOException {
+    if (base == null) {
+      return null;
+    }
     Property prop = base.getChildByName("reference");
     if (prop.hasValues()) {
       String ref = prop.getValues().get(0).primitiveValue();
@@ -195,7 +198,7 @@ public class BundleRenderer extends ResourceRenderer {
     Resource subject = resolveReference(b, comp.getSubject());
     if (subject != null) {
       XhtmlNode nx = (subject instanceof DomainResource) ? ((DomainResource) subject).getText().getDiv() : null;
-      if (nx != null) {
+      if (nx != null && !nx.isEmpty()) {
         x.addChildren(nx);        
       } else {
         RendererFactory.factory(subject, context).render(x, subject);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ConceptMapRenderer.java

@@ -159,9 +159,9 @@ public class ConceptMapRenderer extends TerminologyRenderer {
           else {
             if (ccm.getRelationshipElement().hasExtension(ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
               String code = ToolingExtensions.readStringExtension(ccm.getRelationshipElement(), ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
-              tr.td().ah(eqpath+"#"+code).tx(presentEquivalenceCode(code));                
+              tr.td().ah(eqpath+"#"+code, code).tx(presentEquivalenceCode(code));                
             } else {
-              tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));
+              tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode(), ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));
             }
           }
           td = tr.td();
@@ -192,7 +192,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
         if (hasRelationships) {
           tr.td().b().tx("Relationship");
         }
-        tr.td().colspan(Integer.toString(1+targets.size())).b().tx("Destination Concept Details");
+        tr.td().colspan(Integer.toString(1+targets.size())).b().tx("Target Concept Details");
         if (comment) {
           tr.td().b().tx("Comment");
         }
@@ -299,9 +299,9 @@ public class ConceptMapRenderer extends TerminologyRenderer {
                 else {
                   if (ccm.getRelationshipElement().hasExtension(ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
                     String code = ToolingExtensions.readStringExtension(ccm.getRelationshipElement(), ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
-                    tr.td().ah(eqpath+"#"+code).tx(presentEquivalenceCode(code));                
+                    tr.td().ah(eqpath+"#"+code, code).tx(presentEquivalenceCode(code));                
                   } else {
-                    tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));
+                    tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode(), ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));
                   }
                 }
               }

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

@@ -5094,6 +5094,9 @@ public class FHIRPathEngine {
     int i2 = -1;
     if (exp.parameterCount() == 2) {
       List<Base> n2 = execute(context, focus, exp.getParameters().get(1), true);
+      if (n2.isEmpty()|| !n2.get(0).isPrimitive() || !Utilities.isInteger(n2.get(0).primitiveValue())) {
+        return new ArrayList<Base>();
+      }
       i2 = Integer.parseInt(n2.get(0).primitiveValue());
     }
 

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

@@ -8,6 +8,7 @@ import org.hl7.fhir.r5.context.IWorkerContext.ICanonicalResourceLocator;
 import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.model.ElementDefinition;
+import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.terminologies.TerminologyClient;
@@ -152,7 +153,7 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
       }
       if (pi != null) {
         context.loadFromPackage(pi, null);
-        return pi.hasCanonical(url);
+        return pi.hasCanonical(url) ||  context.fetchResource(Resource.class, url) != null;
       }
     }
 

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

@@ -2402,7 +2402,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                 r = loadContainedResource(errors, path, hostContext.getRootResource(), url.substring(1), Resource.class);
               }
               if (r == null) {
-                fetcher.fetchCanonicalResource(this, url);
+               r = fetcher.fetchCanonicalResource(this, url);
               }
               if (r == null) {
                 r = this.context.fetchResource(Resource.class, url);
@@ -5660,7 +5660,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       msg = fpe.forLog();
     } catch (Exception ex) {
       ok = false;
-      msg = ex.getMessage();
+      msg = ex.getClass().getName()+": "+ex.getMessage();
+      ex.printStackTrace();
     }
     if (!ok) {
       if (!Utilities.noString(msg)) {