patient and visit extensions implemented

histream-import/src/main/java/de/sekmi/histream/etl/ETLObservationSupplier.java

@@ -14,6 +14,7 @@ import de.sekmi.histream.etl.config.PatientTable;
 import de.sekmi.histream.etl.config.VisitTable;
 import de.sekmi.histream.etl.config.WideTable;
 import de.sekmi.histream.ext.Patient;
+import de.sekmi.histream.ext.Visit;
 
 /**
  * Supplier for observations which are loaded from arbitrary
@@ -71,7 +72,10 @@ public class ETLObservationSupplier implements ObservationSupplier{
 		try{
 			pr = pt.open(factory);
 			vr = vt.open(factory);
-			queue = new FactGroupingQueue(pr, vr, factory.getExtensionAccessor(Patient.class), ds.getMeta().getSource());
+			queue = new FactGroupingQueue(pr, vr, 
+					factory.getExtensionAccessor(Patient.class), 
+					factory.getExtensionAccessor(Visit.class), 
+					ds.getMeta().getSource());
 
 			// open all tables
 			wr = new ArrayList<>(wt.size());

histream-import/src/main/java/de/sekmi/histream/etl/FactGroupingQueue.java

@@ -10,6 +10,7 @@ import de.sekmi.histream.ExtensionAccessor;
 import de.sekmi.histream.Observation;
 import de.sekmi.histream.ext.ExternalSourceType;
 import de.sekmi.histream.ext.Patient;
+import de.sekmi.histream.ext.Visit;
 
 /**
  * Algorithm:
@@ -23,15 +24,20 @@ import de.sekmi.histream.ext.Patient;
  *
  */
 public class FactGroupingQueue{
-	private RecordSupplier<? extends FactRow> patientTable, visitTable;
+	private RecordSupplier<PatientRow> patientTable;
+	private RecordSupplier<VisitRow> visitTable;
 	private ExtensionAccessor<Patient> patientAccessor;
+	private ExtensionAccessor<Visit> visitAccessor;
 
 	private ExternalSourceType metaSource;
 	private List<RecordSupplier<? extends FactRow>> factTables;
 
 
-	private FactRow currentPatient, nextVisit;
+	private PatientRow currentPatient;
+	private VisitRow nextVisit;
+	
 	private Patient currentPatientInstance;
+	private Visit currentVisitInstance;
 
 	private String currentVisitId;
 	private List<FactRow> currentRows;
@@ -58,10 +64,12 @@ public class FactGroupingQueue{
 	}
 
 
-	public FactGroupingQueue(RecordSupplier<? extends FactRow> patientTable, RecordSupplier<? extends FactRow>visitTable, ExtensionAccessor<Patient> patientAccessor, ExternalSourceType metaSource){
+	public FactGroupingQueue(RecordSupplier<PatientRow> patientTable, RecordSupplier<VisitRow>visitTable, ExtensionAccessor<Patient> patientAccessor, ExtensionAccessor<Visit> visitAccessor, ExternalSourceType metaSource){
 		this.patientTable = patientTable;
-		this.patientAccessor = patientAccessor;
 		Objects.requireNonNull(patientAccessor);
+		Objects.requireNonNull(visitAccessor);
+		this.patientAccessor = patientAccessor;
+		this.visitAccessor = visitAccessor;
 		this.visitTable = visitTable;
 		this.factTables = new ArrayList<>();
 		this.workQueue = new ArrayDeque<>();
@@ -78,7 +86,11 @@ public class FactGroupingQueue{
 	 */
 	private void patientChanged(){
 		currentPatientInstance = patientAccessor.accessStatic(currentPatient.getPatientId(), metaSource);
-		// TODO sync patient with extension factory
+		currentPatientInstance.setBirthDate(currentPatient.getBirthDate());
+		currentPatientInstance.setDeathDate(currentPatient.getDeathDate());
+		currentPatientInstance.setSex(currentPatient.getSex());
+		// TODO sync patient with extension factory / add fields
+		
 		addFactsToWorkQueue(currentPatient);
 	}
 
@@ -88,12 +100,18 @@ public class FactGroupingQueue{
 	 * If {@link #currentVisitId} is not null, nextVisit will contain the current visit's information.
 	 */
 	private void visitChanged(){
-		// TODO for facts contained in visit, add facts to work queue
 
 		if( currentVisitId == null ){
 			// set visit extension to null
+			// TODO later support facts without encounter
 		}else{
-			// TODO sync visit with extension factory
+			// sync visit with extension factory
+			currentVisitInstance = visitAccessor.accessStatic(currentVisitId, currentPatientInstance, metaSource);
+			currentVisitInstance.setStartTime(nextVisit.getStartTime());
+			currentVisitInstance.setEndTime(nextVisit.getEndTime());
+			currentVisitInstance.setLocationId(nextVisit.getLocationId());
+			currentVisitInstance.setStatus(nextVisit.getStatus());
+			
 			addFactsToWorkQueue(nextVisit);
 		}
 	}
@@ -124,6 +142,7 @@ public class FactGroupingQueue{
 		for( Observation f : r.getFacts() ){
 			// set patient extension
 			patientAccessor.set(f, currentPatientInstance);
+			visitAccessor.set(f, currentVisitInstance);
 			workQueue.add(f);
 		}
 	}

histream-import/src/main/java/de/sekmi/histream/etl/config/VisitTable.java

@@ -28,6 +28,7 @@ public class VisitTable extends Table<VisitRow> implements ConceptTable{
 		StringColumn visitId;
 		DateTimeColumn start;
 		DateTimeColumn end;
+		StringColumn location;
 		// TODO inpatient/outpatient state
 		Column<?>[] ignore;
 	}
@@ -39,6 +40,9 @@ public class VisitTable extends Table<VisitRow> implements ConceptTable{
 		map.registerColumn(idat.visitId);
 		map.registerColumn(idat.start);
 		map.registerColumn(idat.end);
+		if( idat.location != null ){
+			map.registerColumn(idat.location);
+		}
 		for( Concept c : concepts ){
 			mapRegisterConcept(map, c);
 		}
@@ -53,6 +57,9 @@ public class VisitTable extends Table<VisitRow> implements ConceptTable{
 		visit.setPatientId(idat.patientId.valueOf(map, row));
 		visit.setStartTime(idat.start.valueOf(map, row));
 		visit.setEndTime(idat.end.valueOf(map, row));
+		if( idat.location != null ){
+			visit.setLocationId(idat.location.valueOf(map, row));
+		}
 		// TODO other 
 		
 		// concepts

histream-import/src/test/java/de/sekmi/histream/etl/TestETLSupplier.java

@@ -10,10 +10,12 @@ import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 
+import de.sekmi.histream.DateTimeAccuracy;
 import de.sekmi.histream.Observation;
 import de.sekmi.histream.ObservationFactory;
 import de.sekmi.histream.etl.config.DataSource;
 import de.sekmi.histream.ext.Patient;
+import de.sekmi.histream.ext.Visit;
 import de.sekmi.histream.impl.ObservationFactoryImpl;
 import de.sekmi.histream.impl.SimplePatientExtension;
 import de.sekmi.histream.impl.SimpleVisitExtension;
@@ -64,7 +66,26 @@ public class TestETLSupplier {
 		Patient p = fact.getExtension(Patient.class);
 		Assert.assertNotNull(p);
 		Assert.assertEquals("p1", p.getId());
+		Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2003-02-01"), p.getBirthDate());
+		Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2003-02-11"), p.getDeathDate());
+
 		// TODO verify other patient information
+
 	}
+	@Test
+	public void testVisitExtension() throws IOException{
+		Observation fact = os.get();
+		Assert.assertNotNull(fact);
+
+		Visit v = fact.getExtension(Visit.class);
+		Assert.assertNotNull(v);
 
+		Assert.assertEquals("v1", v.getId());
+		// TODO make sure custom partial date format is parsed correctly
+		//Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2013-03-20T09:00"), v.getStartTime());
+		Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2013-03-21T13:00:21"), v.getEndTime());
+
+		Assert.assertEquals("v1", v.getId());
+		Assert.assertEquals(null, v.getLocationId());
+	}
 }