added implementation of stream metadata

histream-core/src/main/java/de/sekmi/histream/Observation.java

@@ -29,6 +29,7 @@ import de.sekmi.histream.ext.ExternalSourceType;
  * Observation of a single event or a single fact assigned to a single patient.
  * 
  * TODO more details
+ * TODO remove ExternalSourceType from interfaces, move to property
  * 
  * @author Raphael
  *

histream-core/src/main/java/de/sekmi/histream/impl/Meta.java

+package de.sekmi.histream.impl;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import de.sekmi.histream.ObservationHandler;
+import de.sekmi.histream.ObservationSupplier;
+
+@XmlRootElement
+@XmlAccessorType(XmlAccessType.FIELD)
+public class Meta {
+	@XmlElement(name="etl-strategy")
+	public String etlStrategy;
+	public ExternalSourceImpl source;
+	public Order order;
+	
+	public static class Order{
+		@XmlAttribute
+		Boolean grouped;
+		@XmlAttribute
+		Boolean sorted;
+		private Order(){}
+		public Order(Boolean grouped, Boolean sorted){
+			this();
+			this.grouped = grouped;
+			this.sorted = sorted;
+		}
+	}
+	
+	/**
+	 * Set meta information via keys from {@link ObservationSupplier}
+	 * @param key key
+	 * @param value value
+	 */
+	public void set(String key, String value){
+		switch( key ){
+		case ObservationSupplier.META_ETL_STRATEGY:
+			this.etlStrategy = value;
+			break;
+		case ObservationSupplier.META_SOURCE_ID:
+			if( source == null )source = new ExternalSourceImpl();
+			source.sourceId = value;
+			break;
+		case ObservationSupplier.META_SOURCE_TIMESTAMP:
+			if( source == null )source = new ExternalSourceImpl();
+			source.sourceTimestamp = javax.xml.bind.DatatypeConverter.parseDateTime(value).toInstant();
+			break;
+		}
+	}
+	
+	public static final void transfer(ObservationSupplier source, ObservationHandler target){
+		String keys[] = new String[]{
+				ObservationSupplier.META_ETL_STRATEGY,
+				ObservationSupplier.META_SOURCE_ID,
+				ObservationSupplier.META_SOURCE_TIMESTAMP
+		};
+		for( String key : keys ){
+			target.setMeta(key, source.getMeta(key));
+		}
+	}
+}

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

@@ -20,6 +20,7 @@ import de.sekmi.histream.ext.ExternalSourceType;
 import de.sekmi.histream.ext.Patient;
 import de.sekmi.histream.ext.Visit;
 import de.sekmi.histream.impl.AbstractObservationHandler;
+import de.sekmi.histream.impl.Meta;
 import de.sekmi.histream.impl.ObservationImpl;
 
 /**
@@ -38,11 +39,13 @@ public class XMLWriter extends AbstractObservationHandler implements Closeable {
 	private XMLStreamWriter writer;
 	private boolean writeFormatted;
 	private int formattingDepth;
+	private Meta meta;
 
 	private XMLWriter() throws JAXBException{
-		this.marshaller = JAXBContext.newInstance(ObservationImpl.class).createMarshaller();
+		this.marshaller = JAXBContext.newInstance(ObservationImpl.class, Meta.class).createMarshaller();
 		marshaller.setProperty(Marshaller.JAXB_FRAGMENT, Boolean.TRUE);
 		this.writeFormatted = true;
+		this.meta = new Meta();
 	}
 	public XMLWriter(OutputStream output) throws JAXBException, XMLStreamException, FactoryConfigurationError{
 		this();
@@ -50,10 +53,9 @@ public class XMLWriter extends AbstractObservationHandler implements Closeable {
 		// enable repairing namespaces to remove duplicate namespace declarations by JAXB marshal
 		factory.setProperty(XMLOutputFactory.IS_REPAIRING_NAMESPACES, Boolean.TRUE);
 		this.writer = factory.createXMLStreamWriter(output);
-		writeStartDocument();
 	}
 
-	private void writeStartDocument() throws XMLStreamException{
+	private void writeStartDocument() throws XMLStreamException, JAXBException{
 		writer.setDefaultNamespace(NAMESPACE);
 		writer.setPrefix("xsi", XMLConstants.W3C_XML_SCHEMA_INSTANCE_NS_URI);
 		writer.writeStartDocument();
@@ -64,11 +66,14 @@ public class XMLWriter extends AbstractObservationHandler implements Closeable {
 		writer.writeNamespace("xsi", XMLConstants.W3C_XML_SCHEMA_INSTANCE_NS_URI);
 		formatNewline();
 		formatPush();
+		
+		formatIndent();
+		marshaller.marshal(meta, writer);
+		formatNewline();
 	}
 	@Override
 	public void setMeta(String key, String value) {
-		// TODO Auto-generated method stub
-
+		meta.set(key, value);
 	}
 	private void formatNewline() throws XMLStreamException{
 		if( writeFormatted )writer.writeCharacters("\n");
@@ -185,7 +190,8 @@ public class XMLWriter extends AbstractObservationHandler implements Closeable {
 		Visit thisVisit = observation.getExtension(Visit.class);
 		try {
 			if( prevPatient == null ){
-				// TODO write start document, meta, patient
+				// write start document, meta, patient
+				writeStartDocument();
 				startPatient(thisPatient);
 			}else if( !prevPatient.getId().equals(thisPatient.getId()) ){
 				// close patient, write new patient

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

@@ -2,8 +2,10 @@ package de.sekmi.histream.io;
 
 import java.io.File;
 import java.io.IOException;
+import java.time.Instant;
 import java.util.stream.StreamSupport;
 
+import javax.xml.bind.JAXB;
 import javax.xml.bind.JAXBException;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
@@ -15,6 +17,8 @@ import org.junit.Test;
 import org.w3c.dom.Document;
 
 import de.sekmi.histream.ObservationSupplier;
+import de.sekmi.histream.impl.ExternalSourceImpl;
+import de.sekmi.histream.impl.Meta;
 
 public class TestXMLWriter {
 
@@ -24,9 +28,22 @@ public class TestXMLWriter {
 		t.initializeObservationFactory();
 		ObservationSupplier s = t.getExampleSupplier();
 		XMLWriter w = new XMLWriter(System.out);
+		Meta.transfer(s, w);
 		StreamSupport.stream(AbstractObservationParser.nonNullSpliterator(s), false).forEach(w);
 		w.close();
 	}
+	
+	@Test
+	public void testWriteMeta(){
+		Meta meta = new Meta();
+		meta.etlStrategy = "lala";
+		meta.source = new ExternalSourceImpl();
+		meta.source.setSourceId("sid");
+		meta.source.setSourceTimestamp(Instant.now());
+		meta.order = new Meta.Order(true,false);
+		
+		JAXB.marshal(meta, System.out);
+	}
 
 	@Test
 	public void testReadWriteIdenticalXML() throws Exception{