Merge branch 'master' of gitlab.uni-oldenburg.de:AKTIN/dwh-import

cda-import/README.md

+CDAs werden transformiert mit cda-eav/*.xsl zu eav-data XML.
+Es ist wichtig, dass bei mehreren CDA-Modulen (die beim gleichen Patient und Fall dokumentiert werden) NICHT die gleichen concept_codes erzeugt werden. Dies wrde unique constraints
+der Tabelle observation_fact verletzen.
+
+
 List of AKTIN module IDs:
 - *base* Basismodul
 - *monitor* berwachung

cda-import/pom.xml

@@ -47,7 +47,6 @@
 					</archive>
 				</configuration>
 			</plugin>
-			-->
 			<plugin>
 				<groupId>org.eclipse.jetty</groupId>
 				<artifactId>jetty-maven-plugin</artifactId>
@@ -60,6 +59,7 @@
 					</dependency>
    				</dependencies>
 			</plugin>
+			-->
 <!-- 
         <plugin>
             <artifactId>maven-dependency-plugin</artifactId>
@@ -89,6 +89,7 @@
 		</plugins>
 	</build>
 	<dependencyManagement>
+	<!--
 		<dependencies>
 			<dependency>
 				<groupId>org.jboss.arquillian</groupId>
@@ -98,6 +99,7 @@
 				<type>pom</type>
 			</dependency>
 		</dependencies>
+		-->
 	</dependencyManagement>
 	<dependencies>
 		<dependency>
@@ -112,10 +114,10 @@
 		<dependency>
 			<groupId>org.aktin</groupId>
 			<artifactId>dwh-api</artifactId>
-			<version>0.2</version>
+			<version>0.3-SNAPSHOT</version>
 		</dependency>
 
-
+<!--
 		<dependency>
 			<groupId>org.jboss.arquillian.junit</groupId>
 			<artifactId>arquillian-junit-container</artifactId>
@@ -135,7 +137,7 @@
 		    <version>2.3.2.Final</version>
 		    <scope>test</scope>
 		</dependency>
-
+-->
 
 
 		<dependency>

cda-import/src/main/java/org/aktin/cda/etl/AbstractCDAImporter.java

@@ -5,6 +5,7 @@ import java.io.InputStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.time.ZoneId;
+import java.util.Date;
 import java.util.function.Consumer;
 
 import javax.xml.bind.JAXBException;
@@ -20,6 +21,7 @@ import org.aktin.cda.CDAStatus.Status;
 import org.aktin.cda.UnsupportedTemplateException;
 import org.aktin.cda.etl.transform.Transformation;
 import org.aktin.cda.etl.transform.TransformationFactory;
+import org.aktin.dwh.Anonymizer;
 import org.w3c.dom.Document;
 
 import de.sekmi.histream.Observation;
@@ -37,14 +39,13 @@ public abstract class AbstractCDAImporter implements CDAProcessor{
 	private TransformationFactory cdaToDataWarehouse;
 	private XMLInputFactory inputFactory;
 
-	public AbstractCDAImporter() throws IOException {
+	public AbstractCDAImporter(Anonymizer anonymizer) throws IOException {
 		// create transformer
 		cdaToDataWarehouse = new TransformationFactory();
-		
+		cdaToDataWarehouse.setAnonymizer(anonymizer);
 		// XML input factory
 		inputFactory = XMLInputFactory.newInstance();
 	}
-
 	
 	/**
 	 * Get the observation factory which will be used to create observations
@@ -91,9 +92,17 @@ public abstract class AbstractCDAImporter implements CDAProcessor{
 			// insert facts
 			suppl.stream().forEach(getObservationInserter());
 			
-			CDAStatus.Status status = deleted?Status.Updated:Status.Created;
+			CDAStatus.Status status;
 			Descriptor desc = new Descriptor(sourceId);
-			// TODO use/write timestamps and version
+			desc.lastModified = new Date();
+			if( deleted ){
+				status = Status.Updated;
+			}else{
+				status = Status.Created;
+				desc.created = desc.lastModified;
+			}
+			
+			// TODO use/write version
 			return new CDAStatus(desc, status);
 		} catch (IOException e) {
 			throw new CDAException("Unable to read EAV temp file: "+file, e);

cda-import/src/main/java/org/aktin/cda/etl/CDAImporter.java

@@ -23,6 +23,7 @@ import org.aktin.cda.CDAException;
 import org.aktin.cda.CDAStatus;
 import org.aktin.cda.CDASummary;
 import org.aktin.cda.DocumentNotFoundException;
+import org.aktin.dwh.Anonymizer;
 import org.aktin.dwh.PreferenceKey;
 import org.w3c.dom.Document;
 
@@ -54,8 +55,8 @@ public class CDAImporter extends AbstractCDAImporter implements AutoCloseable{
 	 * @throws IOException unable to load CDA to ETL transformation script
 	 */
 	@Inject // TODO change to ObservationFactory and see if this works
-	public CDAImporter(ObservationFactory factory, Preferences prefs) throws NamingException, SQLException, IOException {
-		super();
+	public CDAImporter(ObservationFactory factory, Preferences prefs, Anonymizer anonymizer) throws NamingException, SQLException, IOException {
+		super(anonymizer);
 		this.factory = factory;
 		this.localZone = ZoneId.of(prefs.get(PreferenceKey.timeZoneId));
 		log.info("Default timezone for CDA documents: "+localZone);
@@ -73,10 +74,6 @@ public class CDAImporter extends AbstractCDAImporter implements AutoCloseable{
 		 */
 		// data dialect
 		DataDialect dd = new DataDialect();
-		String tz = prefs.get("i2b2.db.tz"); // TODO use PreferenceKey enum
-		if( tz != null ){
-			dd.setTimeZone(ZoneId.of(tz));
-		}
 		try{
 			inserter = new I2b2Inserter();
 			inserter.open(crcDS.getConnection(), dd);

cda-import/src/main/java/org/aktin/cda/etl/Descriptor.java

@@ -6,6 +6,8 @@ import org.aktin.cda.CDASummary;
 
 public class Descriptor implements CDASummary {
 	private String docId;
+	Date lastModified;
+	Date created;
 	
 	public Descriptor(String docId){
 		this.docId = docId;
@@ -17,14 +19,12 @@ public class Descriptor implements CDASummary {
 
 	@Override
 	public Date getLastModified() {
-		// TODO Auto-generated method stub
-		return null;
+		return lastModified;
 	}
 
 	@Override
 	public Date getCreated() {
-		// TODO Auto-generated method stub
-		return null;
+		return created;
 	}
 
 	@Override

cda-import/src/main/java/org/aktin/cda/etl/transform/Transformation.java

@@ -16,6 +16,7 @@ import javax.xml.transform.stream.StreamResult;
 import org.aktin.cda.etl.transform.fun.CalculateEncounterHash;
 import org.aktin.cda.etl.transform.fun.CalculatePatientHash;
 import org.aktin.cda.etl.transform.fun.CalculateSourceId;
+import org.aktin.dwh.Anonymizer;
 import org.w3c.dom.Document;
 
 import net.sf.saxon.Configuration;
@@ -32,6 +33,7 @@ public class Transformation {
 	
 	private TransformerFactoryImpl transformerFactory;
 	private Templates transformerTemplates;
+	private Anonymizer anonymizer;
 
 	/**
 	 * Construct a CDA template to EAV transformation
@@ -42,10 +44,10 @@ public class Transformation {
 	 * @throws TransformerFactoryConfigurationError if the transformer factory failed to initialize
 	 * @throws TransformerConfigurationException  transformer setup error
 	 */
-	public Transformation(String moduleId, String templateId, Document xslt)throws TransformerFactoryConfigurationError, TransformerConfigurationException{
+	public Transformation(String moduleId, String templateId, Document xslt, Anonymizer anonymizer)throws TransformerFactoryConfigurationError, TransformerConfigurationException{
 		this.moduleId = moduleId;
 		this.templateId = templateId;
-		
+		this.anonymizer = anonymizer;
 		// create transformer
 		// ususally a transformer is created via TransformerFactory.newInstance(),
 		// but this may return a non-saxon parser
@@ -70,9 +72,9 @@ public class Transformation {
 //		}
 //		Configuration config = ((TransformerFactoryImpl)factory).getConfiguration();
 		Configuration config = transformerFactory.getConfiguration();
-		config.registerExtensionFunction(new CalculatePatientHash());
-		config.registerExtensionFunction(new CalculateEncounterHash());
-		config.registerExtensionFunction(new CalculateSourceId());
+		config.registerExtensionFunction(new CalculatePatientHash(anonymizer));
+		config.registerExtensionFunction(new CalculateEncounterHash(anonymizer));
+		config.registerExtensionFunction(new CalculateSourceId(anonymizer));
 		// TODO don't need moduleId and factory?
 	}
 

cda-import/src/main/java/org/aktin/cda/etl/transform/TransformationFactory.java

@@ -22,6 +22,7 @@ import javax.xml.xpath.XPathExpressionException;
 import javax.xml.xpath.XPathFactory;
 
 import org.aktin.cda.NamespaceContextImpl;
+import org.aktin.dwh.Anonymizer;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
@@ -38,7 +39,8 @@ public class TransformationFactory {
 	private Map<String, Transformation> cache;
 	private XPath xpath;
 	private DocumentBuilderFactory builderFactory;
-	
+	private Anonymizer anonymizer;
+
 	public TransformationFactory(){
 //		inputFactory = XMLInputFactory.newInstance();
 		// XPath configuration
@@ -77,6 +79,7 @@ public class TransformationFactory {
 	}
 
 	private Transformation loadTransformation(String templateId) throws IOException, TransformerConfigurationException, TransformerFactoryConfigurationError{
+		Objects.requireNonNull(this.anonymizer, "no anonymizer configured");
 		// need to locate the transformation
 		URL url = locateTransformationByTemplate(templateId);
 		if( url == null ){
@@ -101,9 +104,12 @@ public class TransformationFactory {
 			// this should be reported to the developers
 			log.warning("Mismatch between template name="+templateId+" and declared template="+declaredTemplate);
 		}
-		return new Transformation(moduleId, templateId, doc);
+		return new Transformation(moduleId, templateId, doc, anonymizer);
 	}
 	
+	public void setAnonymizer(Anonymizer anonymizer){
+		this.anonymizer = anonymizer;
+	}
 	public Transformation getTransformation(String templateId) throws IOException, TransformerConfigurationException, TransformerFactoryConfigurationError{
 		// look in cache
 		Transformation transform = cache.get(templateId);

cda-import/src/main/java/org/aktin/cda/etl/transform/fun/CalculateEncounterHash.java

 package org.aktin.cda.etl.transform.fun;
 
+import org.aktin.dwh.Anonymizer;
+
 import net.sf.saxon.om.StructuredQName;
 import net.sf.saxon.value.SequenceType;
 
 public class CalculateEncounterHash extends OneWayHashFunction{
+	public CalculateEncounterHash(Anonymizer anonymizer) {
+		super(anonymizer);
+	}
+
 	public static final StructuredQName QNAME = OneWayHashFunction.buildFunctionQName("encounter-hash");
 	protected static final SequenceType[] TWO_STRINGS = new SequenceType[]{SequenceType.SINGLE_STRING,SequenceType.SINGLE_STRING};
 	

cda-import/src/main/java/org/aktin/cda/etl/transform/fun/CalculatePatientHash.java

 package org.aktin.cda.etl.transform.fun;
 
+import org.aktin.dwh.Anonymizer;
+
 import net.sf.saxon.om.StructuredQName;
 import net.sf.saxon.value.SequenceType;
 
 public class CalculatePatientHash extends OneWayHashFunction{
+	public CalculatePatientHash(Anonymizer anonymizer) {
+		super(anonymizer);
+	}
+
 	public static final StructuredQName QNAME = OneWayHashFunction.buildFunctionQName("patient-hash");
 	protected static final SequenceType[] TWO_STRINGS = new SequenceType[]{SequenceType.SINGLE_STRING,SequenceType.SINGLE_STRING};
-	
+
 	@Override
 	public StructuredQName getFunctionQName() {
 		return QNAME;

cda-import/src/main/java/org/aktin/cda/etl/transform/fun/CalculateSourceId.java

 package org.aktin.cda.etl.transform.fun;
 
+import org.aktin.dwh.Anonymizer;
+
 import net.sf.saxon.om.StructuredQName;
 import net.sf.saxon.value.SequenceType;
 
@@ -28,6 +30,10 @@ import net.sf.saxon.value.SequenceType;
  *
  */
 public class CalculateSourceId extends OneWayHashFunction{
+	public CalculateSourceId(Anonymizer anonymizer) {
+		super(anonymizer);
+	}
+
 	public static final StructuredQName QNAME = OneWayHashFunction.buildFunctionQName("import-hash");
 	protected static final SequenceType[] FIVE_STRINGS = new SequenceType[]{SequenceType.SINGLE_STRING,SequenceType.SINGLE_STRING,SequenceType.SINGLE_STRING,SequenceType.SINGLE_STRING,SequenceType.SINGLE_STRING};
 	

cda-import/src/main/java/org/aktin/cda/etl/transform/fun/OneWayHashFunction.java

 package org.aktin.cda.etl.transform.fun;
 
-import java.nio.ByteBuffer;
-import java.nio.charset.Charset;
-import java.security.DigestException;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
-import java.util.Base64;
-import java.util.logging.Logger;
+import org.aktin.dwh.Anonymizer;
 
 import net.sf.saxon.expr.XPathContext;
 import net.sf.saxon.lib.ExtensionFunctionCall;
@@ -24,9 +18,13 @@ import net.sf.saxon.value.StringValue;
  *
  */
 public abstract class OneWayHashFunction extends ExtensionFunctionDefinition {
-	private static final Logger log = Logger.getLogger(OneWayHashFunction.class.getName());
+//	private static final Logger log = Logger.getLogger(OneWayHashFunction.class.getName());
 	public static final String AKTIN_CDA_FUNCTIONS_NS = "http://aktin.org/cda/functions";
-	
+	private Anonymizer anonymizer;
+
+	public OneWayHashFunction(Anonymizer anonymizer){
+		this.anonymizer = anonymizer;
+	}
 	protected static final StructuredQName buildFunctionQName(String funcName){
 		return new StructuredQName("", AKTIN_CDA_FUNCTIONS_NS, funcName);
 	}
@@ -36,40 +34,6 @@ public abstract class OneWayHashFunction extends ExtensionFunctionDefinition {
 		return SequenceType.SINGLE_STRING;
 	}
 	
-	/**
-	 * Calculate a one way hash function for the given input.
-	 * The algorithm is as follows:
-	 * <ol>
-	 *  <li>Concatenate the arguments with a slash (/) as separator.</li>
-	 *  <li>Encode the input arguments with UTF-8 encoding
-	 *  <li>Generate a 160bit SHA-1 checksum</li>
-	 *  <li>Produce bas64 encoding with url-safe alphabet</li>
-	 * </ol>
-	 * The resulting string length will be less than 30 characters.
-	 * 
-	 * @param strings input
-	 * @return string hash
-	 * @throws DigestException error calculating message digest 
-	 */
-	public String calculateHash(String ...strings) throws DigestException{
-		MessageDigest digest;
-		try {
-			digest = MessageDigest.getInstance("SHA-1");
-		} catch (NoSuchAlgorithmException e) {
-			// should not happen. SHA-1 is guaranteed to be included in the JRE
-			throw new DigestException(e);
-		}
-		// join arguments
-		String composite = String.join("/", strings);
-		// logging
-		// encode to bytes
-		ByteBuffer input = Charset.forName("UTF-8").encode(composite);
-		// calculate digest and encode with base64
-		digest.update(input);
-		String result = Base64.getUrlEncoder().encodeToString(digest.digest());
-		log.info("Hash "+getFunctionQName().getDisplayName()+": "+composite+" -> "+result);
-		return result;
-	}
 
 	/**
 	 * Implements a call to the hash function with variable arguments.
@@ -89,11 +53,7 @@ public abstract class OneWayHashFunction extends ExtensionFunctionDefinition {
 			if( arguments.length == 0 ){
 				throw new XPathException("Need at least one argument for hash calculation");
 			}
-			try {
-				return new StringValue(calculateHash(strings));
-			} catch (DigestException e) {
-				throw new XPathException("Unable to calculate hash", e);
-			}
+			return new StringValue(anonymizer.calculateAbstractPseudonym(strings));
 		}
 	}
 

cda-import/src/main/resources/cda-eav/1.2.276.0.76.10.1015.xsl

@@ -141,6 +141,7 @@
                     <!-- Alle Fact-Templates auf Body/Component/Section Ebene aufrufen -->
                     <xsl:apply-templates select="/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section"/>     
                     <xsl:apply-templates select="/cda:ClinicalDocument/cda:componentOf/cda:encompassingEncounter/cda:id[2]"/> 
+                    <xsl:apply-templates select="/cda:ClinicalDocument/cda:templateId"/>
                 </encounter>
             </patient>     
         </eav-data> 
@@ -1000,6 +1001,10 @@
         <xsl:template match="/cda:ClinicalDocument/cda:templateId">
             <xsl:comment>Import Transformation/Version Information</xsl:comment>
             <fact>
+            	<!-- ACHTUNG: in anderen Modulen (z.B. Traumamodul) darf das nachfolgende fact nicht
+            	    genauso ausgegeben werden, da dann die Möglichkeit besteht dass das unique constraint
+            	    der observation_fact tabelle verletzt wird. Da die Software-Version aber gleich ist,
+            	    kann dies komplett weggelassen werden. -->
                 <xsl:attribute name="concept">
                     <xsl:value-of select="$ProjectVersion-Prefix"/><xsl:value-of select="$aktin.release.version"/>
                 </xsl:attribute>

cda-import/src/main/resources/cda-eav/1.2.276.0.76.10.1019.xsl

@@ -141,7 +141,8 @@
                     <xsl:apply-templates select="/cda:ClinicalDocument/cda:participant/cda:associatedEntity"/>   
                     <!-- Alle Fact-Templates auf Body/Component/Section Ebene aufrufen -->
                     <xsl:apply-templates select="/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section"/>                                                    
-                </encounter>
+                    <xsl:apply-templates select="/cda:ClinicalDocument/cda:templateId"/>
+                 </encounter>
             </patient>     
         </eav-data> 
     </xsl:template>
@@ -975,6 +976,10 @@
         <xsl:template match="/cda:ClinicalDocument/cda:templateId">
             <xsl:comment>Import Transformation/Version Information</xsl:comment>
             <fact>
+            	<!-- ACHTUNG: in anderen Modulen (z.B. Traumamodul) darf das nachfolgende fact nicht
+            	    genauso ausgegeben werden, da dann die Möglichkeit besteht dass das unique constraint
+            	    der observation_fact tabelle verletzt wird. Da die Software-Version aber gleich ist,
+            	    kann dies komplett weggelassen werden. -->
                 <xsl:attribute name="concept">
                     <xsl:value-of select="$ProjectVersion-Prefix"/><xsl:value-of select="$aktin.release.version"/>
                 </xsl:attribute>

cda-import/src/test/java/org/aktin/cda/etl/CDAImporterMockUp.java

@@ -24,7 +24,7 @@ public class CDAImporterMockUp extends AbstractCDAImporter implements Consumer<O
 	private int insertCount;
 
 	public CDAImporterMockUp() throws IOException{
-		super();
+		super(new ConcatAnonymizer());
 		System.out.println("CONSTRUCT CDAImporterMockUp");
 		factory = new ObservationFactoryImpl(new SimplePatientExtension(), new SimpleVisitExtension());
 		insertCount = 0;

cda-import/src/test/java/org/aktin/cda/etl/ConcatAnonymizer.java

+package org.aktin.cda.etl;
+
+import org.aktin.dwh.Anonymizer;
+
+/**
+ * Anonymizer for testing. Concatenates the source parts to
+ * produce a pseudonym string which should not be used for
+ * production.
+ * @author R.W.Majeed
+ *
+ */
+public class ConcatAnonymizer implements Anonymizer {
+
+	@Override
+	public String calculateAbstractPseudonym(String... parts) {
+		return String.join("/", parts);
+	}
+
+}

cda-import/src/test/java/org/aktin/cda/etl/TestEEInject.java

-package org.aktin.cda.etl;
-
-import javax.inject.Inject;
-
-import org.aktin.cda.CDAProcessor;
-import org.aktin.cda.etl.xds.DocumentRepository;
-import org.jboss.arquillian.container.test.api.Deployment;
-import org.jboss.arquillian.junit.Arquillian;
-import org.jboss.shrinkwrap.api.ShrinkWrap;
-import org.jboss.shrinkwrap.api.asset.EmptyAsset;
-import org.jboss.shrinkwrap.api.spec.WebArchive;
-import org.junit.Assert;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-
-
-@RunWith(Arquillian.class)
-public class TestEEInject {
-	//private static final String WEBINF_DIR = "src/main/webapp/WEB-INF";
-	@Deployment
-    public static WebArchive createDeployment() {
-        return ShrinkWrap.create(WebArchive.class)
-        		//.addPackage("org.aktin.cda")
-        		.addPackage(CDAProcessor.class.getPackage())
- //       		.addPackage(RestService.class.getPackage())
-        		.addPackage(DocumentRepository.class.getPackage())
-        		.addClass(CDAImporterMockUp.class)
-        		.addAsManifestResource(EmptyAsset.INSTANCE, "META-INF/beans.xml")
-        		//.setWebXML(new File(WEBINF_DIR,"web.xml"))
-        		//.addAsManifestResource(EmptyAsset.INSTANCE, "beans.xml")
-        		//.addAsWebInfResource(new File(WEBINF_DIR,"sun-jaxws.xml"))
-        		;
-    }
-	
-	@Inject
-	private DocumentRepository xdsService;
-	
-	@Test
-	public void verifyInjectedBeans(){
-//		Assert.assertNotNull(restService);
-		Assert.assertNotNull(xdsService);
-		// TODO verify that CDAProcessor instanceof CDAImporter
-	}
-	@Test
-	public void assumeCorrectValidation(){
-		// TODO submit document to services
-	}
-
-}

cda-import/src/test/java/org/aktin/cda/etl/TestTransformationLoader.java

@@ -10,6 +10,7 @@ public class TestTransformationLoader {
 	@Test
 	public void verifyTransformVariables() throws Exception{
 		TransformationFactory f = new TransformationFactory();
+		f.setAnonymizer(new ConcatAnonymizer());
 		//XMLStreamReader xsr = inputFactory.createXMLStreamReader(getClass().getResourceAsStream("/cda-eav.xsl"));
 //		InputSource input = new InputSource(getClass().getResourceAsStream("/cda-eav.xsl"));
 		Transformation t = f.getTransformation("1.2.276.0.76.10.1019");

cda-server/src/main/java/org/aktin/cda/etl/fhir/Binary.java

@@ -3,7 +3,6 @@ package org.aktin.cda.etl.fhir;
 import java.io.BufferedWriter;
 import java.io.IOException;
 import java.net.URI;
-import java.net.URISyntaxException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Paths;
@@ -136,6 +135,7 @@ public class Binary implements ExternalInterface{
 		String templateId = null;
 		boolean isValid = false;
 		boolean importSuccessful = false;
+		URI location = null;
 		Document cda=null;
 		try {
 			cda = parser.buildDOM(doc);
@@ -153,20 +153,18 @@ public class Binary implements ExternalInterface{
 				// otherwise return HTTP_BAD_REQUEST
 				// process document
 				CDAStatus stat = processor.createOrUpdate(cda, documentId, templateId);
-				
 				// check whether document was created or updated, return 201 or 200
 				if( stat.getStatus() == Status.Created ){
-					try {
-						URI location = new URI("Binary/?_id="+stat.getDocumentId());
-						response = Response.created(location);
-					} catch (URISyntaxException e) {
-						log.log(Level.WARNING, "Unable to build URI for created resource", e);
-						response = Response.ok();
-					}
+					// create location conforming to FHIR specification
+					location = URI.create("Binary/"+stat.getDocumentId()+"/_history/0");
+					response = Response.created(location);
+					
 					hallihallo2.addCreated();
 					importSuccessful = true;
 				}else if( stat.getStatus() == Status.Updated ){
 					response = Response.ok();
+					location = URI.create("Binary/"+stat.getDocumentId());
+					// Location header not allowed for status 200
 					hallihallo2.addUpdated();
 					importSuccessful = true;
 				}else{

cda-server/src/main/java/org/aktin/cda/etl/fhir/SimplifiedOperationOutcome.java

@@ -65,6 +65,7 @@ public class SimplifiedOperationOutcome {
 	public static class Issue{
 		Severity severity;
 		String details;
+		String diagnostics;
 		IssueType code;
 		public Issue(Severity severity, IssueType type, String details){
 			this.severity = severity;
@@ -86,6 +87,11 @@ public class SimplifiedOperationOutcome {
 				break;
 			}
 		}
+		public static Issue diagnosticInfo(String message){
+			Issue i = new Issue(Severity.information, IssueType.informational, null);
+			i.diagnostics = "all ok";
+			return i;
+		}
 	}
 	
 	private List<Issue> issues;
@@ -109,7 +115,25 @@ public class SimplifiedOperationOutcome {
 	public void addIssue(Severity severity, IssueType type, String details){
 		issues.add(new Issue(severity, details));
 	}
-	
+
+	private void writeIssue(XMLStreamWriter writer, Issue issue) throws XMLStreamException{
+		writer.writeStartElement("issue");
+		// severity
+		writer.writeStartElement("severity");
+		writer.writeAttribute("value", issue.severity.name());
+		writer.writeEndElement();