observation supplier supports patient extension

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

@@ -50,8 +50,7 @@ public class SimplePatientExtension implements Extension<PatientImpl>{
 
 	@Override
 	public PatientImpl createInstance(Observation observation) {
-		PatientImpl patient = createInstance();
-		patient.setId(observation.getPatientId());
+		PatientImpl patient = createInstance(observation.getPatientId(), observation);
 		return patient;
 	}
 

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

@@ -13,6 +13,7 @@ import de.sekmi.histream.etl.config.DataSource;
 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;
 
 /**
  * Supplier for observations which are loaded from arbitrary
@@ -64,12 +65,13 @@ public class ETLObservationSupplier implements ObservationSupplier{
 		pt = ds.getPatientTable();
 		vt = ds.getVisitTable();
 		wt = ds.getWideTables();
+		// TODO long tables
 
 		// in case of exception, make sure already opened suppliers are closed
 		try{
 			pr = pt.open(factory);
 			vr = vt.open(factory);
-			queue = new FactGroupingQueue(pr, vr);
+			queue = new FactGroupingQueue(pr, vr, factory.getExtensionAccessor(Patient.class), ds.getMeta().getSource());
 
 			// open all tables
 			wr = new ArrayList<>(wt.size());

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

@@ -3,9 +3,13 @@ package de.sekmi.histream.etl;
 import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 import java.util.Queue;
 
+import de.sekmi.histream.ExtensionAccessor;
 import de.sekmi.histream.Observation;
+import de.sekmi.histream.ext.ExternalSourceType;
+import de.sekmi.histream.ext.Patient;
 
 /**
  * Algorithm:
@@ -20,9 +24,15 @@ import de.sekmi.histream.Observation;
  */
 public class FactGroupingQueue{
 	private RecordSupplier<? extends FactRow> patientTable, visitTable;
+	private ExtensionAccessor<Patient> patientAccessor;
+
+	private ExternalSourceType metaSource;
 	private List<RecordSupplier<? extends FactRow>> factTables;
-	
+
+
 	private FactRow currentPatient, nextVisit;
+	private Patient currentPatientInstance;
+
 	private String currentVisitId;
 	private List<FactRow> currentRows;
 	private Queue<Observation> workQueue;
@@ -48,12 +58,14 @@ public class FactGroupingQueue{
 	}
 
 
-	public FactGroupingQueue(RecordSupplier<? extends FactRow> patientTable, RecordSupplier<? extends FactRow>visitTable){
+	public FactGroupingQueue(RecordSupplier<? extends FactRow> patientTable, RecordSupplier<? extends FactRow>visitTable, ExtensionAccessor<Patient> patientAccessor, ExternalSourceType metaSource){
 		this.patientTable = patientTable;
+		this.patientAccessor = patientAccessor;
+		Objects.requireNonNull(patientAccessor);
 		this.visitTable = visitTable;
 		this.factTables = new ArrayList<>();
 		this.workQueue = new ArrayDeque<>();
-		
+		this.metaSource = metaSource;
 	}
 	public void addFactTable(RecordSupplier<? extends FactRow> supplier){
 		if( supplier == patientTable || supplier == visitTable )throw new IllegalArgumentException("Cannot add patient or visit table as fact table");
@@ -61,6 +73,31 @@ public class FactGroupingQueue{
 		factTables.add(supplier);
 	}
 	
+	/**
+	 * Current patient changed: {@link #currentPatient}
+	 */
+	private void patientChanged(){
+		currentPatientInstance = patientAccessor.accessStatic(currentPatient.getPatientId(), metaSource);
+		// TODO sync patient with extension factory
+		addFactsToWorkQueue(currentPatient);
+	}
+
+	/**
+	 * Current visit changed. Current visit id is in {@link #currentVisitId}.
+	 * For facts without visit information, {@link #currentVisitId} may be null.
+	 * 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
+		}else{
+			// TODO sync visit with extension factory
+			addFactsToWorkQueue(nextVisit);
+		}
+	}
+
 	/**
 	 * Load first row from each table, fill and sort the observation queue
 	 */
@@ -74,17 +111,19 @@ public class FactGroupingQueue{
 		tableIndex = 0;
 		
 		currentPatient = patientTable.get();
-		// TODO sync patient with extension factory
-		addFactsToWorkQueue(currentPatient);
+		patientChanged();
 		
 		// for every patient, facts without visitId (=null) are parsed first
 		currentVisitId = null;		
+		visitChanged();
+		
 		nextVisit = visitTable.get();
-		// TODO sync visit with extension factory
 	}
 	
 	private void addFactsToWorkQueue(FactRow r){
 		for( Observation f : r.getFacts() ){
+			// set patient extension
+			patientAccessor.set(f, currentPatientInstance);
 			workQueue.add(f);
 		}
 	}
@@ -126,8 +165,8 @@ public class FactGroupingQueue{
 			if( nextVisit != null && nextVisit.getPatientId().equals(currentPatient.getPatientId()) ){
 				// next visit also belongs to current patient, continue
 				currentVisitId = nextVisit.getVisitId();
-				// TODO: sync visit with extension factory
-				addFactsToWorkQueue(nextVisit);
+				visitChanged();
+				
 				nextVisit = visitTable.get();
 				tableIndex = 0;
 				// goto top
@@ -141,8 +180,9 @@ public class FactGroupingQueue{
 					// we are done
 					break;
 				}
-				// TODO: sync patient with extension factory
-				addFactsToWorkQueue(currentPatient);
+				patientChanged();
+				visitChanged();
+				
 				tableIndex = 0;
 				// goto top
 				continue;

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

@@ -5,32 +5,46 @@ import java.io.InputStream;
 
 import javax.xml.bind.JAXB;
 
+import org.junit.After;
+import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 
 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.impl.ObservationFactoryImpl;
+import de.sekmi.histream.impl.SimplePatientExtension;
+import de.sekmi.histream.impl.SimpleVisitExtension;
 
 public class TestETLSupplier {
 	private DataSource ds;
-	private ObservationFactory of;
+	private ObservationFactory of ;
+	private ETLObservationSupplier os;
 	
 	@Before
-	public void loadConfiguration() throws IOException{
+	public void loadConfiguration() throws IOException, ParseException{
 		try( InputStream in = getClass().getResourceAsStream("/test-1-datasource.xml") ){
 			ds = JAXB.unmarshal(in, DataSource.class);
 		}
 		of = new ObservationFactoryImpl();
+		of.registerExtension(new SimplePatientExtension());
+		of.registerExtension(new SimpleVisitExtension());
+		os = new ETLObservationSupplier(ds,of);
 	}
 
+	@After
+	public void freeResources() throws IOException{
+		os.close();		
+	}
+	
 	@Test
-	public void testReadFacts() throws IOException, ParseException{
-		ETLObservationSupplier s = new ETLObservationSupplier(ds,of);
+	public void testReadFacts() throws IOException{
 		while( true ){
-			Observation fact = s.get();
+			Observation fact = os.get();
 			if( fact == null )break;
+			
 			StringBuilder debug_str = new StringBuilder();
 			debug_str.append(fact.getPatientId()).append('\t');
 			debug_str.append(fact.getEncounterId()).append('\t');
@@ -41,6 +55,16 @@ public class TestETLSupplier {
 			System.out.println(debug_str.toString());
 			// TODO test patient extension, visit extension
 		}
-		s.close();
 	}
+	
+	@Test
+	public void testPatientExtension() throws IOException{
+		Observation fact = os.get();
+		Assert.assertNotNull(fact);
+		Patient p = fact.getExtension(Patient.class);
+		Assert.assertNotNull(p);
+		Assert.assertEquals("p1", p.getId());
+		// TODO verify other patient information
+	}
+
 }

histream-import/src/test/java/de/sekmi/histream/etl/config/TestReadTables.java

@@ -38,7 +38,7 @@ public class TestReadTables {
 	public void testReadPatients() throws IOException, ParseException{
 		try( RecordSupplier<PatientRow> s = ds.patientTable.open(of) ){
 			PatientRow r = s.get();
-			Assert.assertEquals("1", r.getId());
+			Assert.assertEquals("p1", r.getId());
 			Assert.assertEquals(2003, r.getBirthDate().get(ChronoField.YEAR));
 			
 		}