Merge pull request #1012 from hapifhir/gg-202211-json-comments

Consistency around rendering comments in examples in IGs

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/elementmodel/TurtleParser.java

@@ -333,7 +333,7 @@ public class TurtleParser extends ParserBase {
       ontology.triple(ontologyId, "owl:versionIRI", ontologyId.replace(FHIR_URI_BASE, FHIR_VERSION_BASE));
 
     Subject subject = section.triple(subjId, "a", "fhir:" + e.getType());
-		subject.linkedPredicate("fhir:nodeRole", "fhir:treeRoot", linkResolver == null ? null : linkResolver.resolvePage("rdf.html#tree-root"));
+		subject.linkedPredicate("fhir:nodeRole", "fhir:treeRoot", linkResolver == null ? null : linkResolver.resolvePage("rdf.html#tree-root"), null);
 
 		for (Element child : e.getChildren()) {
 			composeElement(section, subject, child, null);
@@ -398,17 +398,17 @@ public class TurtleParser extends ParserBase {
 	  Complex t;
 	  if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY && parent != null && parent.getNamedChildValue("fullUrl") != null) {
 	    String url = "<"+parent.getNamedChildValue("fullUrl")+">";
-	    ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
+	    ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), null);
 	    t = section.subject(url);
 	  } else {
-	    t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
+	    t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), null);
 	  }
     if (element.getSpecial() != null)
-      t.linkedPredicate("a", "fhir:"+element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()));
+      t.linkedPredicate("a", "fhir:"+element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()), null);
 	  if (element.hasValue())
-	  	t.linkedPredicate("fhir:value", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()));
+	  	t.linkedPredicate("fhir:value", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()), null);
 	  if (element.getProperty().isList() && (!element.isResource() || element.getSpecial() == SpecialElement.CONTAINED))
-	  	t.linkedPredicate("fhir:index", Integer.toString(element.getIndex()), linkResolver == null ? null : linkResolver.resolvePage("rdf.html#index"));
+	  	t.linkedPredicate("fhir:index", Integer.toString(element.getIndex()), linkResolver == null ? null : linkResolver.resolvePage("rdf.html#index"), null);
 
 	  if ("Coding".equals(element.getType()))
 	  	decorateCoding(t, element, section);

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

@@ -54,6 +54,7 @@ import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonCreator;
 import org.hl7.fhir.r5.formats.JsonCreatorCanonical;
+import org.hl7.fhir.r5.formats.JsonCreatorDirect;
 import org.hl7.fhir.r5.formats.JsonCreatorGson;
 import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
@@ -182,10 +183,10 @@ public class JsonParser extends ParserBase {
   }
 
   private void checkComments(JsonElement element, Element b, String path) throws FHIRFormatError {
-    if (element.hasComments()) {
+    if (element != null && element.hasComments()) {
       if (allowComments) {
         for (JsonComment c : element.getComments()) {
-          b.getFormatCommentsPre().add(c.getContent());
+          b.getComments().add(c.getContent());
         }
       } else {
         for (JsonComment c : element.getComments()) {
@@ -322,7 +323,7 @@ public class JsonParser extends ParserBase {
       }
       int c = 0;
       for (JsonElement am : arr) {
-        parseChildComplexInstance(npath+"["+c+"]", fpath+"["+c+"]", element, property, name, am);
+        parseChildComplexInstance(npath+"["+c+"]", fpath+"["+c+"]", element, property, name, am, c == 0 ? arr : null, path);
         c++;
       }
     } else if (property.isJsonKeyArray()) {
@@ -394,7 +395,7 @@ public class JsonParser extends ParserBase {
               if (propV.isPrimitive(pvl.getType(null))) {
                 parseChildPrimitiveInstance(n, pvl, pvl.getName(), npathV, fpathV, pv.getValue(), null);
               } else if (pv.getValue() instanceof JsonObject || pv.getValue() instanceof JsonNull) {
-                parseChildComplexInstance(npathV, fpathV, n, pvl, pvl.getName(), pv.getValue());
+                parseChildComplexInstance(npathV, fpathV, n, pvl, pvl.getName(), pv.getValue(), null, null);
               } else {
                 logError(ValidationMessage.NO_RULE_DATE, line(e), col(e), npath, IssueType.INVALID, context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE_AN_OBJECT_NOT_, describe(pv.getValue())), IssueSeverity.ERROR);                       
               }
@@ -407,7 +408,7 @@ public class JsonParser extends ParserBase {
       if (property.isList()) {
         logError(ValidationMessage.NO_RULE_DATE, line(e), col(e), npath, IssueType.INVALID, context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE_AN_ARRAY_NOT_, describe(e), name, path), IssueSeverity.ERROR);
       }
-      parseChildComplexInstance(npath, fpath, element, property, name, e);
+      parseChildComplexInstance(npath, fpath, element, property, name, e, null, null);
     }
   }
 
@@ -419,7 +420,7 @@ public class JsonParser extends ParserBase {
     return b.toString();
   }
 
-  private void parseChildComplexInstance(String npath, String fpath, Element element, Property property, String name, JsonElement e) throws FHIRException {
+  private void parseChildComplexInstance(String npath, String fpath, Element element, Property property, String name, JsonElement e, JsonElement commentContext, String commentPath) throws FHIRException {
     if (property.hasTypeSpecifier()) {
       FHIRPathEngine fpe = new FHIRPathEngine(context);
       String type = null;
@@ -454,6 +455,7 @@ public class JsonParser extends ParserBase {
       JsonObject child = (JsonObject) e;
       Element n = new Element(name, property).markLocation(line(child), col(child));
       n.setPath(fpath);
+      checkComments(commentContext, n, commentPath);        
       checkObject(child, n, npath);
       element.getChildren().add(n);
       if (property.isResource()) {
@@ -465,6 +467,7 @@ public class JsonParser extends ParserBase {
       // we create an element marked as a null element so we know something was present
       JsonNull child = (JsonNull) e;
       Element n = new Element(name, property).markLocation(line(child), col(child));
+      checkComments(commentContext, n, commentPath);        
       checkComments(child, n, fpath);
       n.setPath(fpath);
       element.getChildren().add(n);
@@ -677,11 +680,14 @@ public class JsonParser extends ParserBase {
     }
 
     OutputStreamWriter osw = new OutputStreamWriter(stream, "UTF-8");
-    if (style == OutputStyle.CANONICAL)
+    if (style == OutputStyle.CANONICAL) {
       json = new JsonCreatorCanonical(osw);
-    else
+    } else if (style == OutputStyle.PRETTY) {
-      json = new JsonCreatorGson(osw);
+      json = new JsonCreatorDirect(osw, true, allowComments);
-    json.setIndent(style == OutputStyle.PRETTY ? "  " : "");
+    } else {
+      json = new JsonCreatorDirect(osw, false, allowComments);
+    }
+    checkComposeComments(e);
     json.beginObject();
     prop("resourceType", e.getType(), null);
     Set<String> done = new HashSet<String>();
@@ -693,12 +699,19 @@ public class JsonParser extends ParserBase {
     osw.flush();
   }
 
+  private void checkComposeComments(Element e) {
+    for (String s : e.getComments()) {
+      json.comment(s);
+    }
+  }
+
   public void compose(Element e, JsonCreator json) throws Exception {
     if (e.getPath() == null) {
       e.populatePaths(null);
     }
     
     this.json = json;
+    checkComposeComments(e);
     json.beginObject();
 
     prop("resourceType", e.getType(), linkResolver == null ? null : linkResolver.resolveProperty(e.getProperty()));
@@ -711,6 +724,7 @@ public class JsonParser extends ParserBase {
   }
 
   private void compose(String path, Element e, Set<String> done, Element child) throws IOException {
+    checkComposeComments(child);
     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

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

@@ -69,6 +69,8 @@ public class TurtleParser extends ParserBase {
 
   private String base;
 
+  private OutputStyle style;
+
   public static String FHIR_URI_BASE = "http://hl7.org/fhir/";
   public static String FHIR_VERSION_BASE = "http://build.fhir.org/";
 
@@ -303,18 +305,16 @@ public class TurtleParser extends ParserBase {
     return en.substring(0, en.lastIndexOf(".")+1)+elementName;
   }
   
-  
   @Override
   public void compose(Element e, OutputStream stream, OutputStyle style, String base) throws IOException, FHIRException {
     this.base = base;
+    this.style = style;
     
 		Turtle ttl = new Turtle();
 		compose(e, ttl, base);
 		ttl.commit(stream, false);
   }
 
-
-
   public void compose(Element e, Turtle ttl, String base) throws FHIRException {
     if (e.getPath() == null) {
       e.populatePaths(null);
@@ -325,8 +325,12 @@ public class TurtleParser extends ParserBase {
     ttl.prefix("owl", "http://www.w3.org/2002/07/owl#");
     ttl.prefix("xsd", "http://www.w3.org/2001/XMLSchema#");
 
-
     Section section = ttl.section("resource");
+    if (style == OutputStyle.PRETTY) {
+      for (String s : e.getComments()) {
+        section.stringComment(s);
+      }
+    }
     String subjId = genSubjectId(e);
 
     String ontologyId = subjId.replace(">", ".ttl>");
@@ -337,7 +341,7 @@ public class TurtleParser extends ParserBase {
       ontology.triple(ontologyId, "owl:versionIRI", ontologyId.replace(FHIR_URI_BASE, FHIR_VERSION_BASE));
 
     Subject subject = section.triple(subjId, "a", "fhir:" + e.getType());
-		subject.linkedPredicate("fhir:nodeRole", "fhir:treeRoot", linkResolver == null ? null : linkResolver.resolvePage("rdf.html#tree-root"));
+		subject.linkedPredicate("fhir:nodeRole", "fhir:treeRoot", linkResolver == null ? null : linkResolver.resolvePage("rdf.html#tree-root"), null);
 
 		for (Element child : e.getChildren()) {
 			composeElement(section, subject, child, null);
@@ -364,13 +368,13 @@ public class TurtleParser extends ParserBase {
   protected void decorateReference(Complex t, Element coding) {
     String refURI = getReferenceURI(coding.getChildValue("reference"));
     if(refURI != null)
-      t.linkedPredicate("fhir:link", refURI, linkResolver == null ? null : linkResolver.resolvePage("rdf.html#reference"));
+      t.linkedPredicate("fhir:link", refURI, linkResolver == null ? null : linkResolver.resolvePage("rdf.html#reference"), null);
   }
   
   protected void decorateCanonical(Complex t, Element canonical) {
     String refURI = getReferenceURI(canonical.primitiveValue());
     if(refURI != null)
-      t.linkedPredicate("fhir:link", refURI, linkResolver == null ? null : linkResolver.resolvePage("rdf.html#reference"));
+      t.linkedPredicate("fhir:link", refURI, linkResolver == null ? null : linkResolver.resolvePage("rdf.html#reference"), null);
   }
   
   private String genSubjectId(Element e) {
@@ -397,26 +401,31 @@ public class TurtleParser extends ParserBase {
   private void composeElement(Section section, Complex ctxt, Element element, Element parent) throws FHIRException {
 //    "Extension".equals(element.getType())?
 //            (element.getProperty().getDefinition().getIsModifier()? "modifierExtension" : "extension") ; 
+   
     String en = getFormalName(element);
 
     if (!wantCompose(parent == null ? "" : parent.getPath(), element)) {
       return;
     }
     
+    String comment = null;
+    if (style == OutputStyle.PRETTY) {
+      comment = String.join(", ", element.getComments());
+    }
 	  Complex t;
 	  if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY && parent != null && parent.getNamedChildValue("fullUrl") != null) {
 	    String url = "<"+parent.getNamedChildValue("fullUrl")+">";
-	    ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
+	    ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment);
 	    t = section.subject(url);
 	  } else {
-	    t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
+	    t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment);
 	  }
     if (element.getSpecial() != null)
-      t.linkedPredicate("a", "fhir:"+element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()));
+      t.linkedPredicate("a", "fhir:"+element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()), null);
 	  if (element.hasValue())
-	  	t.linkedPredicate("fhir:value", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()));
+	  	t.linkedPredicate("fhir:value", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()), null);
 	  if (element.getProperty().isList() && (!element.isResource() || element.getSpecial() == SpecialElement.CONTAINED))
-	  	t.linkedPredicate("fhir:index", Integer.toString(element.getIndex()), linkResolver == null ? null : linkResolver.resolvePage("rdf.html#index"));
+	  	t.linkedPredicate("fhir:index", Integer.toString(element.getIndex()), linkResolver == null ? null : linkResolver.resolvePage("rdf.html#index"), null);
 
 	  if ("Coding".equals(element.getType()))
 	  	decorateCoding(t, element, section);
@@ -549,6 +558,12 @@ public class TurtleParser extends ParserBase {
     Expression expression = SnomedExpressions.parse(code);
     
   }
+  public OutputStyle getStyle() {
+    return style;
+  }
+  public void setStyle(OutputStyle style) {
+    this.style = style;
+  }
 
 
 //    128045006|cellulitis (disorder)|:{363698007|finding site|=56459004|foot structure|}

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/JsonCreator.java

@@ -42,7 +42,7 @@ import java.math.BigDecimal;
  */
 public interface JsonCreator {
 
-  void setIndent(String string);
+  void comment(String comment);
   
   void beginObject() throws IOException;
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/JsonCreatorCanonical.java

@@ -116,7 +116,7 @@ public class JsonCreatorCanonical implements JsonCreator {
   
   public JsonCreatorCanonical(OutputStreamWriter osw) {
     stack = new Stack<JsonCreatorCanonical.JsonCanObject>();
-    jj = new JsonCreatorDirect(osw);
+    jj = new JsonCreatorDirect(osw, false, false);
     name = null;
   }
 
@@ -126,13 +126,6 @@ public class JsonCreatorCanonical implements JsonCreator {
     return res;
   }
 
-  @Override
-  public void setIndent(String indent) {
-    if (!indent.equals(""))
-      throw new Error("do not use pretty when canonical is set");
-    jj.setIndent(indent);
-  }
-
   @Override
   public void beginObject() throws IOException {
     JsonCanObject obj = new JsonCanObject(takeName(), false);
@@ -277,5 +270,11 @@ public class JsonCreatorCanonical implements JsonCreator {
     // not used
   }
 
+  @Override
+  public void comment(String content) {
+    // canonical JSON ignores comments
+    
+  }
+       
     
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/JsonCreatorDirect.java

@@ -49,18 +49,24 @@ public class JsonCreatorDirect implements JsonCreator {
 
   private Writer writer;
   private boolean pretty;
+  private boolean comments;
   private boolean named;
   private List<Boolean> valued = new ArrayList<Boolean>();
   private int indent;
+  private List<String> commentList = new ArrayList<>(); 
   
-  public JsonCreatorDirect(Writer writer) {
+  public JsonCreatorDirect(Writer writer, boolean pretty, boolean comments) {
     super();
     this.writer = writer;
+    this.pretty = pretty;
+    this.comments = pretty && comments;
   }
 
   @Override
-  public void setIndent(String indent) {
+  public void comment(String content) {
-    this.pretty = !Utilities.noString(indent);
+    if (comments) {
+      commentList.add(content);
+    }
   }
 
   @Override
@@ -74,6 +80,21 @@ public class JsonCreatorDirect implements JsonCreator {
     valued.add(0, false);
   }
 
+  private void commitComments() throws IOException {
+    if (comments) {
+      for (String s : commentList) {
+        writer.write("// ");
+        writer.write(s);
+        writer.write("\r\n");
+        for (int i = 0; i < indent; i++) {
+          writer.write("  ");
+        }
+      }
+      commentList.clear();
+    }
+  }
+
+
   public void stepIn() throws IOException {
     if (pretty) {
       indent++;
@@ -95,6 +116,7 @@ public class JsonCreatorDirect implements JsonCreator {
   }
 
   private void checkState() throws IOException {
+    commitComments();
     if (named) {
       if (pretty)
         writer.write(" : ");

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/JsonCreatorGson.java

@@ -45,11 +45,6 @@ public class JsonCreatorGson implements JsonCreator {
     gson = new JsonWriter(osw);
   }
 
-  @Override
-  public void setIndent(String indent) {
-    gson.setIndent(indent);
-  }
-
   @Override
   public void beginObject() throws IOException {
     gson.beginObject();    
@@ -121,4 +116,10 @@ public class JsonCreatorGson implements JsonCreator {
     // not used
   }
 
+  @Override
+  public void comment(String content) {
+     // gson (dense json) ignores comments
+    
+  }
+       
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/JsonParserBase.java

@@ -183,11 +183,13 @@ public abstract class JsonParserBase extends ParserBase implements IParser {
   @Override
   public void compose(OutputStream stream, Resource resource) throws IOException {
     OutputStreamWriter osw = new OutputStreamWriter(stream, "UTF-8");
-    if (style == OutputStyle.CANONICAL)
+    if (style == OutputStyle.CANONICAL) {
       json = new JsonCreatorCanonical(osw);
-    else
+    } else if (style == OutputStyle.PRETTY) {
-      json = new JsonCreatorDirect(osw); // use this instead of Gson because this preserves decimal formatting
+      json = new JsonCreatorDirect(osw, true, false);
-    json.setIndent(style == OutputStyle.PRETTY ? "  " : "");
+    } else {
+      json = new JsonCreatorDirect(osw, false, false); // use this instead of Gson because this preserves decimal formatting
+    }
     json.beginObject();
     composeResource(resource);
     json.endObject();
@@ -207,11 +209,13 @@ public abstract class JsonParserBase extends ParserBase implements IParser {
   @Override
   public void compose(OutputStream stream, DataType type, String rootName) throws IOException {
     OutputStreamWriter osw = new OutputStreamWriter(stream, "UTF-8");
-    if (style == OutputStyle.CANONICAL)
+    if (style == OutputStyle.CANONICAL) {
       json = new JsonCreatorCanonical(osw);
-    else
+    } else if (style == OutputStyle.PRETTY) {
-      json = new JsonCreatorDirect(osw);// use this instead of Gson because this preserves decimal formatting
+      json = new JsonCreatorDirect(osw, true, false);
-    json.setIndent(style == OutputStyle.PRETTY ? "  " : "");
+    } else {
+      json = new JsonCreatorDirect(osw, false, false); // use this instead of Gson because this preserves decimal formatting
+    }
     json.beginObject();
     composeTypeInner(type);
     json.endObject();

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/JsonDirectTests.java

@@ -41,7 +41,7 @@ public class JsonDirectTests {
   @Test
   public void testEmptyObject() throws FHIRFormatError, FileNotFoundException, IOException {
     ByteArrayOutputStream bs = new ByteArrayOutputStream();
-    JsonCreatorDirect json = new JsonCreatorDirect(new OutputStreamWriter(bs, "UTF-8"));
+    JsonCreatorDirect json = new JsonCreatorDirect(new OutputStreamWriter(bs, "UTF-8"), false, false);
     json.beginObject();
     json.name("a");
     json.beginObject();

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/turtle/Turtle.java

@@ -77,10 +77,10 @@ public class Turtle {
 			return predicate(predicate, new StringType(object));
 		}
 
-    public Complex linkedPredicate(String predicate, String object, String link) {
+    public Complex linkedPredicate(String predicate, String object, String link, String comment) {
       predicateSet.add(predicate);
       objectSet.add(object);
-      return linkedPredicate(predicate, new StringType(object), link);
+      return linkedPredicate(predicate, new StringType(object), link, comment);
     }
 
 		public Complex predicate(String predicate, Triple object) {
@@ -104,12 +104,13 @@ public class Turtle {
       return null;
     }
 
-    public Complex linkedPredicate(String predicate, Triple object, String link) {
+    public Complex linkedPredicate(String predicate, Triple object, String link, String comment) {
       Predicate p = getPredicate(predicate);
       if (p == null) {
         p = new Predicate();
       p.predicate = predicate;
       p.link = link;
+      p.comment = comment;
       predicateSet.add(predicate);
         predicates.add(p);
       }
@@ -126,10 +127,10 @@ public class Turtle {
 			return c;
 		}
 
-    public Complex linkedPredicate(String predicate, String link) {
+    public Complex linkedPredicate(String predicate, String link, String comment) {
       predicateSet.add(predicate);
       Complex c = complex();
-      linkedPredicate(predicate, c, link);
+      linkedPredicate(predicate, c, link, comment);
       return c;
     }
 
@@ -197,6 +198,7 @@ public class Turtle {
 	}
 
 	public class Section {
+	  private List<String> comments = new ArrayList<>();
 		private String name;
 		private List<Subject> subjects = new ArrayList<Subject>();
 
@@ -244,6 +246,10 @@ public class Turtle {
           return true;
       return false;
     }
+
+    public void stringComment(String cnt) {
+      comments.add(cnt);
+    }
 	}
 
 	private List<Section> sections = new ArrayList<Section>();
@@ -437,6 +443,12 @@ public class Turtle {
 	private void commitSection(LineOutputStreamWriter writer, Section section) throws IOException {
 	  writer.ln("# - "+section.name+" "+Utilities.padLeft("", '-', 75-section.name.length()));
 	  writer.ln();
+	  if (!section.comments.isEmpty()) {
+	    for (String s : section.comments) {
+	      writer.ln("# "+s);		  
+	    }
+	    writer.ln();
+	  }
 		for (Subject sbj : section.subjects) {
       if (Utilities.noString(sbj.id)) {
         writer.write("[");
@@ -447,6 +459,7 @@ public class Turtle {
 			int i = 0;
 
 			for (Predicate p : sbj.predicates) {
+			  //
 				writer.write(p.getPredicate());
 				writer.write(" ");
         boolean first = true;
@@ -481,12 +494,19 @@ public class Turtle {
   private void commitSection(StringBuilder b, Section section) throws Exception {
     b.append("# - "+section.name+" "+Utilities.padLeft("", '-', 75-section.name.length())+"\r\n");
     b.append("\r\n");
+    if (!section.comments.isEmpty()) {
+      for (String s : section.comments) {
+        b.append("# "+s+"\r\n");      
+      }
+      b.append("\r\n");
+    }
     for (Subject sbj : section.subjects) {
       b.append(Utilities.escapeXml(sbj.id));
       b.append(" ");
       int i = 0;
 
       for (Predicate p : sbj.predicates) {
+        //        b.append("# test\r\n ");      
         b.append(p.makelink());
         b.append(" ");
         boolean first = true;

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XMLWriter.java

@@ -480,9 +480,9 @@ public class XMLWriter extends OutputStreamWriter implements IXMLWriter {
 			writePretty();
 		}
 		if (levels.inComment())
-			write("<!-- "+comment+" -- >");
+			write("  <!-- "+comment+" -- >");
 		else
-			write("<!-- "+comment+" -->");
+			write("  <!-- "+comment+" -->");
 		if (doPretty && !isPretty())
 			writePretty();
 	}