Support for rendering contained resources in IG Publisher

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

@@ -79,6 +79,15 @@ private Map<String, Object> userData;
     return (Integer) getUserData(name);
   }
 
+  public void copyUserData(Base other) {
+    if (other.userData != null) {
+      if (userData == null) {
+        userData = new HashMap<>();
+      }
+      userData.putAll(other.userData);
+    }
+  }      
+
   public boolean hasFormatComment() {
   	return (formatCommentsPre != null && !formatCommentsPre.isEmpty()) || (formatCommentsPost != null && !formatCommentsPost.isEmpty());
   }

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

@@ -0,0 +1,65 @@
+package org.hl7.fhir.r5.test;
+
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+
+import org.hl7.fhir.r5.context.SimpleWorkerContext;
+import org.hl7.fhir.r5.elementmodel.Element;
+import org.hl7.fhir.r5.elementmodel.Manager;
+import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
+import org.hl7.fhir.r5.utils.FHIRPathEngine;
+import org.hl7.fhir.utilities.cache.PackageCacheManager;
+import org.hl7.fhir.utilities.cache.ToolsVersion;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+
+public class XmlParserTests {
+
+  private static SimpleWorkerContext context;
+  private static FHIRPathEngine fp;
+
+  @BeforeAll
+  public static void setUp() throws Exception {
+    PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
+    context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
+    fp = new FHIRPathEngine(context);
+
+    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "any.xml"), "any.xml", null);
+    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ii.xml"), "ii.xml", null);
+    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cd.xml"), "cd.xml", null);
+    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ce.xml"), "ce.xml", null);
+    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ed.xml"), "ed.xml", null);
+    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "st.xml"), "st.xml", null);
+    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cda.xml"), "cda.xml", null);
+    for (StructureDefinition sd : context.getStructures()) {
+      if (!sd.hasSnapshot()) {
+        System.out.println("generate snapshot for " + sd.getUrl());
+        context.generateSnapshot(sd, true);
+      }
+    }
+  }
+
+  @Test
+  /**
+   * Deserializes a simplified CDA example into the logical model and checks that
+   * xml deserialization works for the xsi:type 
+   * 
+   * @throws IOException
+   */
+  public void testXsiDeserialiserXmlParser() throws IOException {
+    Element cda = Manager.parse(context, TestingUtilities.loadTestResourceStream("validator", "cda", "example-xsi.xml"),
+        FhirFormat.XML);
+
+    ByteArrayOutputStream baosXml = new  ByteArrayOutputStream();
+    Manager.compose(context, cda, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);  
+
+    String cdaSerialised = baosXml.toString();
+    assertTrue(cdaSerialised.indexOf("xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"")>0);
+    assertTrue(cdaSerialised.indexOf("xsi:type=\"CD\"")>0); 
+  }
+} 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java

@@ -917,4 +917,12 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
     if (!check)
       throw new FHIRException(message);
   }
+
+  public void emptyRow(TableModel model, int cellCount) {
+    Row r = new Row();
+    model.rows.add(r);
+    for (int i = 0; i < cellCount; i++) {
+      r.getCells().add(new Cell());
+    }
+  }
 }