Add round trip tests and add fix for round-tripping issue

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/JavaParserJsonGenerator.java

@@ -436,10 +436,12 @@ public class JavaParserJsonGenerator extends JavaBaseGenerator {
           }
 
           if (isPrimitive(ed) || ed.typeSummary().startsWith("canonical(")) {
-            composer.append("        openArray(\""+name+"\");\r\n");
+            composer.append("        if (anyHasValue(element.get"+upFirst(getElementName(name, false))+"())) {\r\n");
-            composer.append("        for ("+(tn.contains("(") ? stn : upFirst(tn))+" e : element.get"+upFirst(getElementName(name, false))+"()) \r\n");
+            composer.append("          openArray(\""+name+"\");\r\n");
-            composer.append("          "+comp+"Core(null, e, true);\r\n");
+            composer.append("          for ("+(tn.contains("(") ? stn : upFirst(tn))+" e : element.get"+upFirst(getElementName(name, false))+"()) \r\n");
-            composer.append("        closeArray();\r\n");
+            composer.append("            "+comp+"Core(null, e, e != element.get"+upFirst(getElementName(name, false))+"().get(element.get"+upFirst(getElementName(name, false))+"().size()-1));\r\n");
+            composer.append("          closeArray();\r\n");
+            composer.append("        }\r\n");
             composer.append("        if (anyHasExtras(element.get"+upFirst(getElementName(name, false))+"())) {\r\n");
             composer.append("          openArray(\"_"+name+"\");\r\n");
             composer.append("          for ("+(stn.contains("(") ? stn : upFirst(stn))+" e : element.get"+upFirst(getElementName(name, false))+"()) \r\n");

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

@@ -72,6 +72,7 @@ import org.hl7.fhir.r5.model.DataType;
 import org.hl7.fhir.r5.model.DomainResource;
 import org.hl7.fhir.r5.model.Element;
 import org.hl7.fhir.r5.model.IdType;
+import org.hl7.fhir.r5.model.PrimitiveType;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.StringType;
 import org.hl7.fhir.utilities.TextFile;
@@ -324,11 +325,19 @@ public abstract class JsonParserBase extends ParserBase implements IParser {
 //  }
 
   protected boolean anyHasExtras(List<? extends Element> list) {
-	  for (Element e : list) {
+    for (Element e : list) {
-	  	if (e.hasExtension() || !Utilities.noString(e.getId()))
+      if (e.hasExtension() || !Utilities.noString(e.getId()))
-	  		return true;
+        return true;
-	  }
+    }
-	  return false;
+    return false;
+  }
+
+  protected boolean anyHasValue(List<? extends PrimitiveType> list) {
+    for (PrimitiveType e : list) {
+      if (e.hasValue())
+        return true;
+    }
+    return false;
   }
 
 	protected boolean makeComments(Element element) {

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

@@ -0,0 +1,98 @@
+package org.hl7.fhir.r5.test;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Stream;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.NotImplementedException;
+import org.hl7.fhir.exceptions.DefinitionException;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.exceptions.PathEngineException;
+import org.hl7.fhir.r5.conformance.ProfileUtilities;
+import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.formats.JsonParser;
+import org.hl7.fhir.r5.formats.XmlParser;
+import org.hl7.fhir.r5.model.Base;
+import org.hl7.fhir.r5.model.Bundle;
+import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
+import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
+import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
+import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
+import org.hl7.fhir.r5.renderers.RendererFactory;
+import org.hl7.fhir.r5.renderers.utils.RenderingContext;
+import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
+import org.hl7.fhir.r5.model.TypeDetails;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
+import org.hl7.fhir.r5.utils.FHIRPathEngine;
+import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
+import org.hl7.fhir.r5.utils.IResourceValidator;
+import org.hl7.fhir.r5.utils.XVerExtensionManager;
+import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.cache.NpmPackage;
+import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
+import org.hl7.fhir.utilities.cache.ToolsVersion;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
+import org.hl7.fhir.utilities.xml.XMLUtil;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+public class ParsingTests {
+
+  private static NpmPackage npm;
+
+  @BeforeAll
+  public static void setUp() {
+  }
+
+  public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
+    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
+    npm = pcm.loadPackage("hl7.fhir.r5.examples", "4.5.0");
+    List<Arguments> objects = new ArrayList<>();
+    List<String> names = npm.list("package");
+    for (String n : names) {
+      if (!n.contains("manifest.json") && !n.contains("xver-") && !n.contains("uml.json")  && !n.contains("package-min-ver.json")) {
+        objects.add(Arguments.of(n));
+      }
+    }
+    return objects.stream();
+  }
+
+  @SuppressWarnings("deprecation")
+  @ParameterizedTest(name = "{index}: file {0}")
+  @MethodSource("data")
+  public void test(String name) throws Exception {
+    System.out.println(name);
+    byte[] b = TextFile.streamToBytes(npm.load("package", name));
+    String src = new String(b);
+    Resource r = new JsonParser().parse(b);
+    b = new XmlParser().composeBytes(r);
+    r = new XmlParser().parse(b);
+    b = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(r);
+    String output = new String(b);
+    String msg = TestingUtilities.checkJsonSrcIsSame(src, output);
+    Assertions.assertTrue(msg == null, msg);
+  }
+
+}