Merge pull request #197 from ahdis/oliveregger_cdatitle

Deserializing CDA ST and ED elements from JSON fix

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/elementmodel/JsonParser.java

@@ -183,7 +183,7 @@ public class JsonParser extends ParserBase {
 	}
 
   public void parseChildItem(String path, JsonObject object, Element context, Set<String> processed, Property property) {
-			if (property.isChoice()) {
+			if (property.isChoice() || property.getDefinition().getPath().endsWith("data[x]")) {
 				for (TypeRefComponent type : property.getDefinition().getType()) {
 					String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode());
 					if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) {

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

@@ -184,7 +184,7 @@ public class JsonParser extends ParserBase {
 	}
 
   public void parseChildItem(String path, JsonObject object, Element context, Set<String> processed, Property property) {
-    if (property.isChoice()) {
+    if (property.isChoice() || property.getDefinition().getPath().endsWith("data[x]")) {
     	for (TypeRefComponent type : property.getDefinition().getType()) {
     		String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode());
     		if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) {

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

@@ -210,6 +210,10 @@ public class XmlParser extends ParserBase {
       return "h:";
     if (ns.equals("urn:hl7-org:v3"))
       return "v3:";
+    if (ns.equals("urn:hl7-org:sdtc")) 
+      return "sdtc:";
+    if (ns.equals("urn:ihe:pharm"))
+      return "pharm:";
     return "?:";
   }
 
@@ -538,9 +542,29 @@ public class XmlParser extends ParserBase {
     xml.setDefaultNamespace(e.getProperty().getXmlNamespace());
     if (hasTypeAttr(e))
       xml.namespace("http://www.w3.org/2001/XMLSchema-instance", "xsi");
+    addNamespaces(xml, e);
     composeElement(xml, e, e.getType(), true);
     xml.end();
+  }
 
+  private void addNamespaces(IXMLWriter xml, Element e) throws IOException {
+    String ns = e.getProperty().getXmlNamespace();
+    if (ns!=null && !xml.getDefaultNamespace().equals(ns)){
+      if (!xml.namespaceDefined(ns)) {
+        String prefix = pathPrefix(ns);
+        if (prefix.endsWith(":")) {
+          prefix = prefix.substring(0, prefix.length()-1);
+        }
+        if ("?".equals(prefix)) {
+          xml.namespace(ns);
+        } else {
+          xml.namespace(ns, prefix);
+        }
+      }
+    }
+    for (Element c : e.getChildren()) {
+      addNamespaces(xml, c);
+    }
   }
   
   private boolean hasTypeAttr(Element e) {
@@ -584,9 +608,9 @@ public class XmlParser extends ParserBase {
     if (isText(element.getProperty())) {
       if (linkResolver != null)
         xml.link(linkResolver.resolveProperty(element.getProperty()));
-      xml.enter(elementName);
+      xml.enter(element.getProperty().getXmlNamespace(),elementName);
       xml.text(element.getValue());
-      xml.exit(elementName);   
+      xml.exit(element.getProperty().getXmlNamespace(),elementName);   
     } else if (!element.hasChildren() && !element.hasValue()) {
       if (element.getExplicitType() != null)
         xml.attribute("xsi:type", element.getExplicitType());
@@ -614,10 +638,10 @@ public class XmlParser extends ParserBase {
         if (linkResolver != null)
           xml.link(linkResolver.resolveProperty(element.getProperty()));
 				if (element.hasChildren()) {
-					xml.enter(elementName);
+				  xml.enter(element.getProperty().getXmlNamespace(), elementName);
-					for (Element child : element.getChildren()) 
+				  for (Element child : element.getChildren()) 
 						composeElement(xml, child, child.getName(), false);
-					xml.exit(elementName);
+					xml.exit(element.getProperty().getXmlNamespace(),elementName);
 				} else
           xml.element(elementName);
       }
@@ -630,16 +654,16 @@ public class XmlParser extends ParserBase {
           String av = child.getValue();
           if (ToolingExtensions.hasExtension(child.getProperty().getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"))
             av = convertForDateFormatToExternal(ToolingExtensions.readStringExtension(child.getProperty().getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"), av);
-          xml.attribute(child.getName(), av);
+          xml.attribute(child.getProperty().getXmlNamespace(),child.getProperty().getXmlName(), av);
-      }
+        }
       }
       if (linkResolver != null)
         xml.link(linkResolver.resolveProperty(element.getProperty()));
-      xml.enter(elementName);
+      xml.enter(element.getProperty().getXmlNamespace(),elementName);
       if (!root && element.getSpecial() != null) {
         if (linkResolver != null)
           xml.link(linkResolver.resolveProperty(element.getProperty()));
-        xml.enter(element.getType());
+        xml.enter(element.getProperty().getXmlNamespace(),element.getType());
       }
       for (Element child : element.getChildren()) {
         if (isText(child.getProperty())) {
@@ -650,8 +674,8 @@ public class XmlParser extends ParserBase {
           composeElement(xml, child, child.getName(), false);
       }
 	    if (!root && element.getSpecial() != null)
-        xml.exit(element.getType());
+        xml.exit(element.getProperty().getXmlNamespace(),element.getType());
-      xml.exit(elementName);
+      xml.exit(element.getProperty().getXmlNamespace(),elementName);
     }
   }
 

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

@@ -1,11 +1,14 @@
 package org.hl7.fhir.r5.test;
 
+import java.io.ByteArrayInputStream;
+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;
@@ -13,22 +16,33 @@ import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.cache.ToolsVersion;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 public class CDARoundTripTests {
 
-//  private SimpleWorkerContext context;
+	private static SimpleWorkerContext context;
-// old-test  private FHIRPathEngine fp;
+	private static FHIRPathEngine fp;
 
-  @BeforeAll
+	@BeforeAll
-  public static void setUp() throws Exception {
+	public static void setUp() throws Exception {
-// old-test     context = new SimpleWorkerContext();
+	    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
-// old-test     PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
+		context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
-// old-test     context.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "dev"), null, "StructureDefinition");
+		fp = new FHIRPathEngine(context);
-// old-test     context.loadFromPackage(pcm.loadPackage("hl7.fhir.cda", "dev"), null, "StructureDefinition");
+
-// old-test     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);
+			}
+		}
+	}
 
 // old-test    
 //  @Test
@@ -172,29 +186,57 @@ public class CDARoundTripTests {
 //        FhirFormat.TURTLE, OutputStyle.PRETTY, null);
 //  }
 
-
+	public void assertsExample(Element cdaExample) {
-  @Test
+	    Assertions.assertEquals("2.16.840.1.113883.3.27.1776", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.templateId.root")));
-  public void testSimple() throws IOException {
+        Assertions.assertEquals("SoEN", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.displayName")));
-    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
+        Assertions.assertEquals("SoEN2", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.sdtcDisplayName")));
-    SimpleWorkerContext context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
+        Assertions.assertEquals("c266", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.id.extension")));
-    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "any.xml"), "any.xml", null);
+	    Assertions.assertEquals("2.16.840.1.113883.19.4", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.id.root")));
-    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ii.xml"), "ii.xml", null);
+	    Assertions.assertEquals("X-34133-9", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.code")));
-    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cd.xml"), "cd.xml", null);
+	    Assertions.assertEquals("2.16.840.1.113883.6.1", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.codeSystem")));
-    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ce.xml"), "ce.xml", null);
+	    Assertions.assertEquals("LOINC", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.codeSystemName")));
-    context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ed.xml"), "ed.xml", null);
+	    Assertions.assertEquals("Episode Note", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.title.dataString")));	  
-    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);
-      }
-    }
-    Element cda = Manager.parse(context, TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"), FhirFormat.XML);
-    FHIRPathEngine fp = new FHIRPathEngine(context);
-    Assertions.assertEquals("2.16.840.1.113883.3.27.1776", fp.evaluateToString(null, cda, cda, cda, fp.parse("ClinicalDocument.templateId.root")));
-    Assertions.assertEquals("SoEN", fp.evaluateToString(null, cda, cda, cda, fp.parse("ClinicalDocument.code.displayName")));
-    Assertions.assertEquals("SoEN2", fp.evaluateToString(null, cda, cda, cda, fp.parse("ClinicalDocument.code.sdtcDisplayName")));
   }
 
+	@Test
+	/**
+	 * Deserializes a simplified CDA example into the logical model and checks that
+	 * xml deserialization/serialization
+	 * 
+	 * @throws IOException
+	 */
+	public void testClinicalDocumentXmlParser() throws IOException {
+		Element cda = Manager.parse(context, TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"),
+				FhirFormat.XML);
+
+		assertsExample(cda);
+
+		ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
+		Manager.compose(context, cda, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
+		Element cdaXmlRoundtrip = Manager.parse(context, new ByteArrayInputStream(baosXml.toString().getBytes()), FhirFormat.XML);
+		assertsExample(cdaXmlRoundtrip);
+	}
+
+	@Test
+	/**
+	 * Deserializes a simplified CDA example into the logical model and checks that
+	 * json deserialization/serialization works
+	 * 
+	 * @throws IOException
+	 */
+	public void testClinicalDocumentJsonParser() throws IOException {
+		Element cda = Manager.parse(context, TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"),
+				FhirFormat.XML);
+
+		assertsExample(cda);
+
+		ByteArrayOutputStream baosJson = new ByteArrayOutputStream();
+		Manager.compose(context, cda, baosJson, FhirFormat.JSON, OutputStyle.PRETTY, null);
+		Element cdaJsonRoundtrip = Manager.parse(context, new ByteArrayInputStream(baosJson.toString().getBytes()),
+				FhirFormat.JSON);
+		
+		assertsExample(cdaJsonRoundtrip);
+
+	}
+
 }