XML writer added

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

+package de.sekmi.histream.io;
+
+import java.io.Closeable;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Map;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLOutputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamWriter;
+
+import de.sekmi.histream.Observation;
+import de.sekmi.histream.ObservationException;
+import de.sekmi.histream.Plugin;
+import de.sekmi.histream.ext.Patient;
+import de.sekmi.histream.ext.Visit;
+import de.sekmi.histream.impl.AbstractObservationHandler;
+import de.sekmi.histream.impl.ObservationImpl;
+
+/**
+ * Writes observations to a single XML file. Observations must be grouped by patient and encounter.
+ * TODO write test case which reads+writes XML file and compares input+output literally.
+ * TODO prevent duplicate namespace declarations by JAXB.marshal of facts
+ * 
+ * @author Raphael
+ *
+ */
+public class XMLWriter extends AbstractObservationHandler implements Closeable, Plugin {
+	private static final String NAMESPACE = "http://sekmi.de/histream/ns/eav-data";
+	private Patient prevPatient;
+	private Visit prevVisit;
+	private Marshaller marshaller;
+	private OutputStream output;
+	private XMLStreamWriter writer;
+	private boolean writeFormatted;
+	private int formattingDepth;
+	
+	public XMLWriter(Map<String,String> config) throws JAXBException, XMLStreamException, FactoryConfigurationError{
+		this.marshaller = JAXBContext.newInstance(ObservationImpl.class).createMarshaller();
+		marshaller.setProperty(Marshaller.JAXB_FRAGMENT, Boolean.TRUE);
+		marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+		this.writeFormatted = true;
+		this.output = System.out;
+		XMLOutputFactory factory = XMLOutputFactory.newFactory();
+
+		this.writer = factory.createXMLStreamWriter(output, "UTF-8");
+		writer.writeStartDocument();
+		formatNewline();
+		writer.setDefaultNamespace(NAMESPACE);
+		//?? writer.setPrefix("xsi", "http://www.w3.org/2001/XMLSchema-instance");
+		writer.writeStartElement(NAMESPACE, JAXBObservationSupplier.DOCUMENT_ROOT);
+		writer.writeDefaultNamespace(NAMESPACE);
+		writer.writeNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance");
+		formatNewline();
+		formatPush();
+		//Transformer transformer = TransformerFactory.newInstance().newTransformer();
+		//transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+		//transformer.
+	}
+	@Override
+	public void setMeta(String key, String value) {
+		// TODO Auto-generated method stub
+
+	}
+	private void formatNewline() throws XMLStreamException{
+		if( writeFormatted )writer.writeCharacters("\n");
+	}
+	private void formatIndent() throws XMLStreamException{
+		if( writeFormatted )for( int i=0; i<formattingDepth; i++ ){
+			writer.writeCharacters("\t");
+		}
+	}
+	private void formatPush(){
+		formattingDepth ++;
+	}
+	private void formatPop(){
+		formattingDepth --;
+	}
+
+	private void startEncounter(Visit visit)throws XMLStreamException{
+		formatIndent();
+		writer.writeStartElement(JAXBObservationSupplier.ENCOUNTER_ELEMENT);
+		writer.writeAttribute("id", visit.getId());
+		formatNewline();
+		formatPush();
+		
+		if( visit.getStartTime() != null ){
+			formatIndent();
+			writer.writeStartElement("start");
+			writer.writeCharacters(visit.getStartTime().toPartialIso8601());
+			writer.writeEndElement();
+			formatNewline();
+		}
+		if( visit.getEndTime() != null ){
+			formatIndent();
+			writer.writeStartElement("end");
+			writer.writeCharacters(visit.getEndTime().toPartialIso8601());
+			writer.writeEndElement();
+			formatNewline();
+		}
+		if( visit.getLocationId() != null ){
+			formatIndent();
+			writer.writeStartElement("location");
+			writer.writeCharacters(visit.getLocationId());
+			writer.writeEndElement();
+			formatNewline();
+		}
+		// TODO implement provider
+
+		// TODO more data
+		formatIndent();
+		writer.writeStartElement(JAXBObservationSupplier.FACT_WRAPPER);
+		formatNewline();
+		formatPush();
+		this.prevVisit = visit;
+	}
+	private void endEncounter() throws XMLStreamException{
+		formatPop();
+		formatIndent();
+		writer.writeEndElement(); // fact wrapper
+		formatNewline();
+		formatPop();
+		formatIndent();
+		writer.writeEndElement(); // encounter
+		formatNewline();
+	}
+	private void endPatient() throws XMLStreamException{
+		formatPop();
+		formatIndent();
+		writer.writeEndElement();
+		formatNewline();
+	}
+	private void startPatient(Patient patient) throws XMLStreamException{
+		formatIndent();
+		writer.writeStartElement(JAXBObservationSupplier.PATIENT_ELEMENT);
+		writer.writeAttribute("id", patient.getId());
+		formatNewline();
+		formatPush();
+		
+		// TODO: how write dedicated source information
+		// write surname
+		// write given name
+		
+		// gender
+		if( patient.getSex() != null ){
+			formatIndent();
+			writer.writeStartElement("gender");
+			// TODO use acronym/special value
+			writer.writeCharacters(patient.getSex().name());
+			writer.writeEndElement();
+			formatNewline();
+		}
+		
+		// birth date
+		if( patient.getBirthDate() != null ){
+			formatIndent();
+			writer.writeStartElement("birthdate");
+			writer.writeCharacters(patient.getBirthDate().toPartialIso8601());
+			writer.writeEndElement();
+			formatNewline();
+		}
+		
+		if( patient.getDeathDate() != null ){
+			formatIndent();
+			writer.writeStartElement("deathdate");
+			writer.writeCharacters(patient.getDeathDate().toPartialIso8601());
+			writer.writeEndElement();
+			formatNewline();
+		}
+		prevPatient = patient;
+		
+		prevVisit = null; // clear previous encounter
+	}
+	@Override
+	protected void acceptOrException(Observation observation) throws ObservationException {
+		Patient thisPatient = observation.getExtension(Patient.class);
+		Visit thisVisit = observation.getExtension(Visit.class);
+		try {
+			if( prevPatient == null ){
+				// TODO write start document, meta, patient
+				startPatient(thisPatient);
+			}else if( !prevPatient.getId().equals(thisPatient.getId()) ){
+				// close patient, write new patient
+				endEncounter();
+				endPatient();
+				startPatient(thisPatient);
+			}else{
+				// same patient as previous fact
+				// nothing to do
+			}
+			
+			if( prevVisit == null ){
+				// first visit for patient
+				startEncounter(thisVisit);
+			}else if( !prevVisit.getId().equals(thisVisit.getId()) ){
+				endEncounter(); // close previous encounter
+				startEncounter(thisVisit);
+			}else{
+				// same encounter as previous fact
+				// nothing to do
+			}
+			// TODO clone observation, remove patient/encounter/source information as it is contained in wrappers
+			formatIndent();
+			marshaller.marshal(observation, writer);
+			formatNewline();
+			
+		} catch (JAXBException | XMLStreamException e ) {
+			throw new ObservationException(observation, e);
+		}
+		
+	}
+	
+	@Override
+	public void close() throws IOException{
+		try {
+			if( prevPatient != null ){
+				// at least one fact processed
+				// end facts, encounter, patient
+				for( int i=0; i<3; i++){
+					formatPop();
+					formatIndent();
+					writer.writeEndElement();
+					formatNewline();
+				}
+			}
+			writer.writeEndDocument(); // automatically closes root element
+			writer.close();
+			output.close();
+		} catch (XMLStreamException e) {
+			throw new IOException(e);
+		}
+	}
+
+}

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

+package de.sekmi.histream.io;
+
+import java.io.IOException;
+import java.util.stream.StreamSupport;
+
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLStreamException;
+
+import org.junit.Test;
+
+import de.sekmi.histream.ObservationSupplier;
+
+public class TestXMLWriter {
+
+	@Test
+	public void testWrite() throws IOException, JAXBException, XMLStreamException, FactoryConfigurationError{
+		FileObservationProviderTest t = new FileObservationProviderTest();
+		t.initializeObservationFactory();
+		ObservationSupplier s = t.getExampleSupplier();
+		XMLWriter w = new XMLWriter(null);
+		StreamSupport.stream(AbstractObservationParser.nonNullSpliterator(s), false).forEach(w);
+		w.close();
+	}
+}