JAXB fact provider uncoupled from old XML fact provider

histream-core/examples/dwh-jaxb.xml

@@ -17,9 +17,11 @@
   limitations under the License.
   #L%
   -->
-<dwh-eav xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" >
+<eav-data xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" >
 	<!-- TODO namespace xmlns="http://sekmi.de/histream/dwh-eav..." -->
-	<!-- chronologisch impliziert, dass der zeitstempel eines nachfolgenden elementes gr��er als alle vorangehenden elemente sein muss. Der Zeitstempel kann vor dem Encounter-Start liegen -->
+	<!-- chronologisch impliziert, dass der zeitstempel eines nachfolgenden elementes 
+	größer als alle vorangehenden elemente sein muss. Der Zeitstempel kann vor dem 
+	Encounter-Start liegen -->
 	<meta>
 		<!-- Zeitpunkt, an dem der Export erstellt wurde bzw. Datenstand -->
 		<etl strategy="replace-visit" />
@@ -27,14 +29,15 @@
 		
 		<!-- weitere metadaten n�tig? wertebereich, datentypen, ontologie, ...? -->
 	</meta>
-	<visit>
-		<patid>XX12345</patid>
+	<patient id="XX12345">
 		<surname>Dampf</surname>
 		<names>A</names>
 		<birthdate>2001-01-01</birthdate>
 		<deathdate>2020</deathdate>
 		<sex>F</sex>
-		<encounter start="2014-01-01T10:30:00" end="2014-01-05T10:30:00">XXE12345</encounter>
+		<encounter id="XXE12345">
+			<start>2014-01-01T10:30:00</start>
+			<end>2014-01-05T10:30:00</end>
 			<location>Zuhause</location>
 			<!-- TODO inpatient/outpatient -->
 			<provider>xxxa</provider>
@@ -69,7 +72,7 @@
 				</fact>
 	
 			</facts>
-	</visit>
-	<!-- weitere zeitstempel -->
+		</encounter>	
+	</patient>
 	
-</dwh-eav>
+</eav-data>

histream-core/examples/histream.xml

@@ -46,6 +46,7 @@
 			<property name="project">demo</property>					
 			<property name="nullProvider">LCS-I2B2:PROVIDERS</property>					
 		</plugin>
+		<!-- supported file formats -->
 		<plugin class="de.sekmi.histream.io.XMLProviderFactory"/>
 		<plugin class="de.sekmi.histream.io.FlatProviderFactory"/>
 		

histream-core/src/main/java/de/sekmi/histream/io/FlatObservationSupplier.java

@@ -208,6 +208,7 @@ public class FlatObservationSupplier extends AbstractObservationParser implement
 	}
 	
 	public FlatObservationSupplier(ObservationFactory factory, InputStream input) throws IOException{
+		// TODO: standard API functionality: close() method will not close InputStream passed in constructor
 		this(factory, new BufferedReader(new InputStreamReader(input)));
 	}
 

histream-core/src/main/java/de/sekmi/histream/io/JAXBObservationSupplier.java

 package de.sekmi.histream.io;
 
+import java.io.IOException;
 import java.io.InputStream;
+import java.io.UncheckedIOException;
+import java.util.HashMap;
+import java.util.Map;
 
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Unmarshaller;
 import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
 
+import de.sekmi.histream.DateTimeAccuracy;
+import de.sekmi.histream.Observation;
+import de.sekmi.histream.ObservationFactory;
+import de.sekmi.histream.ObservationSupplier;
+import de.sekmi.histream.impl.ObservationImpl;
 
+public class JAXBObservationSupplier implements ObservationSupplier {
+	private static final String DOCUMENT_ROOT = "eav-data";
+	private static final String PATIENT_ELEMENT = "patient";
+	private static final String ENCOUNTER_ELEMENT = "encounter";
+	private static final String FACT_WRAPPER = "facts";
 	
 	
 
+	private ObservationFactory factory;
+	private Unmarshaller unmarshaller;
+	private XMLStreamReader reader;
+	private Map<String,String> meta;
+	// patient data
+	private String patientId;
+	private Map<String,String> patientData;
 	
-import de.sekmi.histream.Observation;
-import de.sekmi.histream.ObservationFactory;
-import de.sekmi.histream.impl.ObservationImpl;
+	// encounter data
+	private String encounterId;
+	private DateTimeAccuracy encounterStart;
+	private DateTimeAccuracy encounterEnd;
+	private Map<String,String> visitData;
 	
-public class JAXBObservationSupplier extends XMLObservationSupplier {
-	private Unmarshaller unmarshaller;
 	
-	public JAXBObservationSupplier(ObservationFactory factory, InputStream input)
-			throws XMLStreamException, FactoryConfigurationError, JAXBException {
-		super(factory, input);
+	
+	
+	public JAXBObservationSupplier(ObservationFactory factory, InputStream input)throws JAXBException, XMLStreamException, FactoryConfigurationError{
+		this(factory, XMLInputFactory.newInstance().createXMLStreamReader(input));
+	}
+	public JAXBObservationSupplier(ObservationFactory factory, XMLStreamReader reader) throws JAXBException, XMLStreamException{
+		this.factory = factory;
+		this.meta = new HashMap<>();
+		this.patientData = new HashMap<>();
+		this.visitData = new HashMap<>();
 		unmarshaller = JAXBContext.newInstance(ObservationImpl.class).createUnmarshaller();
+		// TODO: set schema
+		//unmarshaller.setSchema(schema);
+		this.reader = reader;
+		readToRoot();
+		readMeta();
+		readPatient();
+		readEncounter();
+	}
 	
+	private void readToRoot() throws XMLStreamException{
+		while( reader.hasNext() ){
+			reader.next();
+			if( reader.isStartElement() )break;
+		}
+		if( !reader.isStartElement() || !reader.getLocalName().equals(DOCUMENT_ROOT) ){
+			throw new XMLStreamException("Start element '"+DOCUMENT_ROOT+"' expected instead of "+reader.getLocalName(), reader.getLocation());
+		}		
+		reader.nextTag();
 	}
 	
-	@Override
+	private void readMeta()throws XMLStreamException{
+		if( !reader.isStartElement() || !reader.getLocalName().equals("meta") )return;
+		
+		// read meta
+		reader.nextTag();
+		if( reader.getLocalName().equals("etl") ){
+			String etlStrategy = reader.getAttributeValue(null, "strategy");
+			// TODO use constants for etl.strategy, etc.
+			if( etlStrategy != null )meta.put("etl.strategy", etlStrategy);
+			reader.nextTag();
+			// should be end element
+			reader.nextTag();
+		}
+		if( reader.getLocalName().equals("source") ){
+			meta.put("source.timestamp", reader.getAttributeValue(null, "timestamp"));
+			meta.put("source.id", reader.getAttributeValue(null, "id"));
+
+			reader.nextTag();
+			// should be end element
+			reader.nextTag();
+		}
+
+		// skip to end of meta
+		while( !reader.isEndElement() || !reader.getLocalName().equals("meta") ){
+			reader.next();
+		}
+		reader.nextTag();
+	}
+
+
+	/**
+	 * Reads patient element with content. Precondition patient start element. Postcondition encounter start element.
+	 * @throws XMLStreamException on error
+	 */
+	private void readPatient() throws XMLStreamException{
+		if( !reader.getLocalName().equals(PATIENT_ELEMENT) ){
+			throw new XMLStreamException("Expected element: "+PATIENT_ELEMENT,reader.getLocation());
+		}
+		patientId = reader.getAttributeValue(null, "id");
+		patientData.clear();
+		reader.nextTag();
+		while( reader.isStartElement() 
+				&& !reader.getLocalName().equals(ENCOUNTER_ELEMENT) )
+		{
+			patientData.put(reader.getLocalName(), reader.getElementText());
+			reader.nextTag();
+		}
+	}
+	/**
+	 * Reads encounter element with content. 
+	 * Precondition encounter start element. 
+	 * Postcondition facts start element.
+	 * @throws XMLStreamException on error
+	 */
+	private void readEncounter() throws XMLStreamException{
+		if( !reader.getLocalName().equals(ENCOUNTER_ELEMENT) ){
+			throw new XMLStreamException("Expected element: "+ENCOUNTER_ELEMENT,reader.getLocation());
+		}
+		visitData.clear();
+		encounterId = reader.getAttributeValue(null, "id");
+		reader.nextTag();
+		while( reader.isStartElement() 
+				&& !reader.getLocalName().equals(FACT_WRAPPER) )
+		{
+			visitData.put(reader.getLocalName(), reader.getElementText());
+			reader.nextTag();
+		}
+		if( visitData.containsKey("start") ){
+			encounterStart = DateTimeAccuracy.parsePartialIso8601(visitData.get("start"));
+		}
+		if( visitData.containsKey("end") ){
+			encounterEnd = DateTimeAccuracy.parsePartialIso8601(visitData.get("end"));
+		}
+		// TODO assert at <facts>
+		reader.nextTag();
+	}
 	protected Observation readObservation()throws XMLStreamException{
 		if( reader.isWhiteSpace() ){
 			reader.nextTag();
@@ -35,42 +157,79 @@ public class JAXBObservationSupplier extends XMLObservationSupplier {
 		// </facts> might occur after previous call to readObservation()
 		while( reader.isEndElement() ){
 			switch( reader.getLocalName() ){
-			case "facts":
+			case FACT_WRAPPER:
 				// end of facts
 				reader.nextTag();
-			case "visit":
+				// fall through to end of visit, 
+				// XXX this doesn't work, if facts are allowed outside of encounter (e.g. directly under patient)
+			case ENCOUNTER_ELEMENT:
 				// end of visit
 				reader.nextTag();
-				if( reader.isStartElement() && reader.getLocalName().equals("visit") ){
+				if( reader.isStartElement() && reader.getLocalName().equals(ENCOUNTER_ELEMENT) ){
 					// next visit
-					readVisit();
+					readEncounter();
+				}
+				break;
+			case PATIENT_ELEMENT:
+				// end of patient
+				reader.nextTag();
+				if( reader.isStartElement() && reader.getLocalName().equals(PATIENT_ELEMENT) ){
+					readPatient();
+					readEncounter();
 				}
 				break;
-			case "dwh-eav":
+			case DOCUMENT_ROOT:
 				// end of document
 				return null;
 			}
 		}
 		// start element of eav-item or eav-group
-		if( !reader.isStartElement() 
-				|| !(reader.getLocalName().equals("fact")) ){
-			throw new XMLStreamException("Element fact expected instead of "+reader.getLocalName(), reader.getLocation());
+		if( !reader.isStartElement() ){
+			throw new XMLStreamException("Element patient, encounter or fact expected instead of "+reader.getLocalName(), reader.getLocation());
+		}
+		if( reader.getLocalName().equals(PATIENT_ELEMENT) ){
+			
 		}
 		ObservationImpl fact;
 		try {
 			fact = (ObservationImpl)unmarshaller.unmarshal(reader);
+			// TODO: set factory
 		} catch (JAXBException e) {
 			throw new XMLStreamException( e);
 		}
-		if( fact.getPatientId() == null ){
-			fact.setPatientId(visitData.get("patid"));
+		if( fact.getPatientId() != null && !fact.getPatientId().equals(patientId) ){
+			throw new XMLStreamException("Fact patid differs from patient id", reader.getLocation());
 		}
+		
+		fact.setPatientId(patientId);
+		fact.setEncounterId(encounterId);
+	
 		if( fact.getStartTime() == null ){
 			fact.setStartTime(encounterStart);
+			fact.setEndTime(encounterEnd);
 		}
 		// TODO set etc. from visit
 		
 		// TODO set ObservationFactory, initialize extensions
 		return fact;
 	}
+
+	@Override
+	public Observation get() {
+		try {
+			return readObservation();
+		} catch (XMLStreamException e) {
+			throw new UncheckedIOException(new IOException(e));
+		}
+	}
+
+	@Override
+	public String getMeta(String key) {
+		return meta.get(key);
+	}
+
+	@Override
+	public void close() throws XMLStreamException {
+		reader.close();
+	}
 }

histream-core/src/test/java/de/sekmi/histream/io/FileObservationProviderTest.java

@@ -199,7 +199,7 @@ public class FileObservationProviderTest {
 	
 	@Test
 	public void testJAXBReader() throws FileNotFoundException, XMLStreamException, FactoryConfigurationError, JAXBException  {
-		XMLObservationSupplier xos = new JAXBObservationSupplier(factory, new FileInputStream("examples/dwh-jaxb.xml"));
+		JAXBObservationSupplier xos = new JAXBObservationSupplier(factory, new FileInputStream("examples/dwh-jaxb.xml"));
 		validateExample(xos);
 		xos.close();
 	}

histream-core/src/test/java/de/sekmi/histream/io/TransformerTest.java

@@ -8,8 +8,6 @@ import org.junit.Test;
 
 
 public class TransformerTest {
-	
-	@SuppressWarnings("resource")
 	@Test
 	public void testPullTransformerIdentity() throws FileNotFoundException, IOException{
 		FileObservationProviderTest f = new FileObservationProviderTest();