XPath expressions for visits can now access the patient via .. (e.g. ../@id)

histream-export/src/main/java/de/sekmi/histream/export/FragmentExporter.java

@@ -6,7 +6,7 @@ import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.xpath.XPath;
 
-import org.w3c.dom.Node;
+import org.w3c.dom.Element;
 
 import de.sekmi.histream.ObservationException;
 import de.sekmi.histream.export.config.ExportDescriptor;
@@ -26,6 +26,7 @@ class FragmentExporter extends VisitFragmentParser {
 
 	TableParser patientParser;
 	TableParser visitParser;
+	private Element currentPatient;
 	
 	protected FragmentExporter(XPath xpath, ExportDescriptor desc, ExportWriter writer) throws ExportException, XMLStreamException, ParserConfigurationException {
 		super();
@@ -39,7 +40,8 @@ class FragmentExporter extends VisitFragmentParser {
 	}
 
 	@Override
-	protected void patientFragment(Node patient) throws ObservationException {
+	protected void patientFragment(Element patient) throws ObservationException {
+		currentPatient = patient;
 		try {
 			patientParser.writeRow(patient);
 		} catch (ExportException | IOException e) {
@@ -48,11 +50,18 @@ class FragmentExporter extends VisitFragmentParser {
 	}
 
 	@Override
-	protected void visitFragment(Node visit) throws ObservationException {
+	protected void visitFragment(Element visit) throws ObservationException {
+		// move visit to patient
+		// this allows XPath expressions to access the patient via
+		// the parent element. E.g. '../@id' to get the patient id
+		currentPatient.appendChild(visit);
 		try {
 			visitParser.writeRow(visit);
 		} catch (ExportException | IOException e) {
 			throw new ObservationException(e);
+		} finally {
+			// remove visit from patient
+			currentPatient.removeChild(visit);
 		}
 		// TODO check for repeating concepts and write to separate parsers
 	}

histream-export/src/main/java/de/sekmi/histream/export/VisitFragmentParser.java

@@ -12,6 +12,7 @@ import javax.xml.transform.dom.DOMResult;
 
 import org.w3c.dom.Document;
 import org.w3c.dom.DocumentFragment;
+import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 
 import de.sekmi.histream.ObservationException;
@@ -74,7 +75,7 @@ abstract class VisitFragmentParser extends GroupedXMLWriter {
 		}else{
 			// No visit for patient.
 			// process patient fragment anyway
-			patientFragment(currentPatient.getFirstChild());
+			patientFragment((Element)currentPatient.getFirstChild());
 		}
 	}
 
@@ -96,7 +97,7 @@ abstract class VisitFragmentParser extends GroupedXMLWriter {
 		if( firstVisit == false ){
 			// patient fragment was parsed
 			fixNamespaces(currentPatient);
-			patientFragment(currentPatient.getFirstChild());
+			patientFragment((Element)currentPatient.getFirstChild());
 			firstVisit = true;
 		}
 
@@ -120,7 +121,7 @@ abstract class VisitFragmentParser extends GroupedXMLWriter {
 		fixNamespaces(currentVisit);
 		Node node = currentVisit.getFirstChild();
 		Objects.requireNonNull(node);
-		visitFragment(currentVisit.getFirstChild());
+		visitFragment((Element)currentVisit.getFirstChild());
 	}
 	/**
 	 * Called after each patient fragment was parsed.
@@ -129,7 +130,7 @@ abstract class VisitFragmentParser extends GroupedXMLWriter {
 	 * @param patient patient node
 	 * @throws ObservationException error
 	 */
-	protected void patientFragment(Node patient)throws ObservationException{
+	protected void patientFragment(Element patient)throws ObservationException{
 		
 	}
 	/**
@@ -139,5 +140,5 @@ abstract class VisitFragmentParser extends GroupedXMLWriter {
 	 * @param visit visit node
 	 * @throws ObservationException error
 	 */
-	protected abstract void visitFragment(Node visit) throws ObservationException;
+	protected abstract void visitFragment(Element visit) throws ObservationException;
 }

histream-export/src/main/java/de/sekmi/histream/export/VisitFragmentSupplier.java

@@ -5,6 +5,7 @@ import java.util.function.Supplier;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.stream.XMLStreamException;
 
+import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 
 import de.sekmi.histream.Observation;
@@ -21,7 +22,7 @@ public class VisitFragmentSupplier implements Supplier<Node> {
 		this.supplier = supplier;
 		this.parser = new VisitFragmentParser() {
 			@Override
-			protected void visitFragment(Node visit) {
+			protected void visitFragment(Element visit) {
 				VisitFragmentSupplier.this.visit = visit;
 			}
 		};

histream-export/src/test/resources/export1.xml

@@ -15,6 +15,7 @@
         <column header="modified" xpath="eav:source/@timestamp"/>
     </patient-table>
     <visit-table>
+        <column header="pid" xpath="../@id"/>
 		<column header="vid" xpath="@id"/>
 		<column header="start" xpath="eav:start"/>
 		<column header="f_start" xpath="eav:fact[@concept='T:full']/@start"/>