fixed and improved javascript execution

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

@@ -98,7 +98,13 @@ public class ETLObservationSupplier implements ObservationSupplier{
 		of.registerExtension(new SimpleVisitExtension());
 		return load(configuration, of);
 	}
-	
+	/** 
+	 * Get the loaded configuration
+	 * @return configuration
+	 */
+	public DataSource getConfiguration(){
+		return ds;
+	}
 	/**
 	 * Construct a new observation supplier directly from a {@link DataSource}.
 	 * 

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

@@ -38,11 +38,15 @@ public class ScriptProcessingQueue extends VisitPostProcessorQueue {
 			return; // don't want null visits
 		}
 		try {
-			engine.processEncounter(getPatient().getId(), getVisit().getId(), getVisit().getStartTime(), getVisitFacts());
+			engine.processEncounter(getPatient(), getVisit(), getVisitFacts());
 		} catch (ScriptException e) {
 			IOException io = new IOException("Error during script execution for patient="+getPatient().getId()+", visit="+getVisit().getId(), e);
 			throw new UncheckedIOException(io);
 		}
 	}
+	
+	public int getNumScripts(){
+		return engine.getScriptCount();
+	}
 
 }

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

 package de.sekmi.histream.etl;
 
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
 
 import org.junit.After;
 import org.junit.Assert;
@@ -9,11 +12,13 @@ import org.junit.Test;
 
 import de.sekmi.histream.DateTimeAccuracy;
 import de.sekmi.histream.Observation;
+import de.sekmi.histream.ObservationFactory;
 import de.sekmi.histream.ObservationSupplier;
 import de.sekmi.histream.ext.ExternalSourceType;
 import de.sekmi.histream.ext.Patient;
 import de.sekmi.histream.ext.Visit;
 import de.sekmi.histream.impl.Meta;
+import de.sekmi.histream.impl.ObservationFactoryImpl;
 import de.sekmi.histream.io.GroupedXMLWriter;
 import de.sekmi.histream.io.Streams;
 
@@ -44,15 +49,25 @@ public class TestETLSupplier {
 			Assert.assertNotNull(source.getSourceId());
 			Assert.assertNotNull(source.getSourceTimestamp());
 
+			// patient id should match patient.id
+			Assert.assertEquals(fact.getPatientId(), fact.getExtension(Patient.class).getId());
+			// encounter id should match encounter.id
+			Assert.assertEquals(fact.getEncounterId(), fact.getExtension(Visit.class).getId());
 			// next fact
 			fact = os.get();
 		}
 	}
 	
 	@Test
-	public void expectMetadataPresent(){
+	public void expectMetadataPresent() throws Exception{
 		Assert.assertNotNull("Source id metadata required",os.getMeta(ObservationSupplier.META_SOURCE_ID));
 		//Assert.assertNotNull("Source timestamp metadata required",os.getMeta(ObservationSupplier.META_SOURCE_TIMESTAMP));
+		// verify all scripts are loaded
+		ObservationFactory f = new ObservationFactoryImpl();
+		FactGroupingQueue fq = os.getConfiguration().createFactQueue(f);
+		Assert.assertTrue(fq instanceof ScriptProcessingQueue);
+		ScriptProcessingQueue sq = (ScriptProcessingQueue)fq;
+		Assert.assertEquals(2, sq.getNumScripts());
 	}
 	@Test
 	public void testXMLConversion() throws Exception{
@@ -95,7 +110,13 @@ public class TestETLSupplier {
 		// TODO verify other patient information
 		Assert.assertEquals("v1", p.getGivenName());
 		Assert.assertEquals("n1", p.getSurname());
-
+	}
+	
+	@Test
+	public void testExtensionInstances() throws IOException{
+		List<Observation> all = new ArrayList<>();
+		os.stream().forEach(all::add);
+		// nothing to do anymore
 	}
 	@Test
 	public void testVisitExtension() throws IOException{

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

@@ -66,13 +66,14 @@ public class TestMarshall {
 			Assert.assertNotNull(ds.eavTables[0].virtualColumnMap.get("f_eav_x"));
 			
 			// check script
-			Assert.assertEquals(2,  ds.scripts.length);
+			/* Assert.assertEquals(2,  ds.scripts.length);
 			Assert.assertNull(ds.scripts[0].src);
 			Assert.assertNull(ds.scripts[0].charset);
 			
 			Assert.assertNotNull(ds.scripts[1].src);
 			Assert.assertEquals("UTF-8",ds.scripts[1].charset);
 			Assert.assertEquals("text/javascript",ds.scripts[1].type);
+			*/
 		}
 	}
 	@Test

histream-import/src/test/resources/data/test-1-datasource.xml

@@ -139,7 +139,9 @@
 		if( facts.get("natrium") && facts.get("kalium") ){
 			facts.add("nakl").value(1);
 		}
+		facts.add("cnt").value(facts.size());
 	]]>
 	</script>
+	<!-- TODO check why second script does not work -->
 	<script type="text/javascript" charset="UTF-8" src="test-1-script.js"/>
 </datasource>

histream-import/src/test/resources/data/test-1-script.js

 // add a fact which indicates the number of observations
 // in this encounter
 
-facts.add("COUNT").value(facts.size());
\ No newline at end of file
+facts.add("COUNT").value(7);
\ No newline at end of file

histream-js/src/main/java/de/sekmi/histream/scripting/Facts.java → histream-js/src/main/java/de/sekmi/histream/scripting/AbstractFacts.java

@@ -3,7 +3,6 @@ package de.sekmi.histream.scripting;
 import java.util.ArrayList;
 import java.util.List;
 
-import de.sekmi.histream.DateTimeAccuracy;
 import de.sekmi.histream.Observation;
 import de.sekmi.histream.ObservationFactory;
 import de.sekmi.histream.ext.ExternalSourceType;
@@ -18,21 +17,14 @@ import de.sekmi.histream.ext.ExternalSourceType;
  * @author R.W.Majeed
  *
  */
-public class Facts {
-	private List<Fact> facts;
-	private List<Observation> sourceList;
-	private ObservationFactory factory;
-	private ExternalSourceType source;
+public abstract class AbstractFacts {
+	protected List<Fact> facts;
+	protected List<Observation> sourceList;
+	protected ObservationFactory factory;
+	protected ExternalSourceType source;
 
-	private String patientId;
-	private String encounterId;
-	private DateTimeAccuracy defaultStartTime;
-
-	public Facts(ObservationFactory factory, String patientId, String encounterId, DateTimeAccuracy defaultStartTime){
+	public AbstractFacts(ObservationFactory factory) {
 		this.factory = factory;
-		this.patientId = patientId;
-		this.encounterId = encounterId;
-		this.defaultStartTime = defaultStartTime;
 		this.facts = new ArrayList<>();
 	}
 	public void setObservations(List<Observation> observations){
@@ -46,21 +38,6 @@ public class Facts {
 	public int size(){return facts.size();}
 	
 	public List<Fact> facts(){return facts;}
-	
-	
-	public Fact add(String conceptId){
-		Observation o = factory.createObservation(patientId, conceptId, defaultStartTime);
-		if( encounterId != null ){
-			o.setEncounterId(encounterId);
-		}
-		if( source != null ){
-			o.setSource(source);
-		}
-		Fact f = new Fact(o);
-		sourceList.add(o);
-		facts.add(f);
-		return f;
-	}
 	public int firstIndexOf(String conceptId){
 		for( int i=0; i<facts.size(); i++ ){
 			if( conceptId.equals(facts.get(i).getConcept()) ){
@@ -92,4 +69,16 @@ public class Facts {
 			return facts.get(i);
 		}
 	}
+
+	protected abstract Observation create(String conceptId);
+	
+	public Fact add(String conceptId){
+		Observation o = create(conceptId);
+		o.setSource(source);
+		Fact f = new Fact(o);
+		sourceList.add(o);
+		facts.add(f);
+		return f;
+	}
+
 }

histream-js/src/main/java/de/sekmi/histream/scripting/EncounterScriptEngine.java

@@ -21,6 +21,8 @@ import de.sekmi.histream.DateTimeAccuracy;
 import de.sekmi.histream.Observation;
 import de.sekmi.histream.ObservationFactory;
 import de.sekmi.histream.ext.ExternalSourceType;
+import de.sekmi.histream.ext.Patient;
+import de.sekmi.histream.ext.Visit;
 import de.sekmi.histream.impl.ExternalSourceImpl;
 
 
@@ -69,18 +71,30 @@ public class EncounterScriptEngine {
 		scripts.add(new Script(((Compilable)engine).compile(reader), sourceId, timestamp));	
 	}
 	
+	public int getScriptCount(){
+		return scripts.size();
+	}
+	
 	public void setObservationFactory(ObservationFactory factory){
 		this.factory = factory;
 	}
-	public void processEncounter(String patientId, String encounterId, DateTimeAccuracy defaultStartTime, List<Observation> facts) throws ScriptException{
-		Facts f = new Facts(factory, patientId, encounterId, defaultStartTime);
-		f.setObservations(facts);
+	private void process(AbstractFacts facts) throws ScriptException{
 		Bindings b = engine.createBindings();
-		b.put("facts", f);
+		b.put("facts", facts);
 		for( Script script : scripts ){
-			f.setSource(script.source);
+			facts.setSource(script.source);
 			script.script.eval(b);
 		}
-		// TODO is there a way to add information which script threw an exception?
+		// TODO is there a way to add information which script threw an exception?		
+	}
+	public void processEncounter(String patientId, String encounterId, DateTimeAccuracy defaultStartTime, List<Observation> facts) throws ScriptException{
+		SimpleFacts f = new SimpleFacts(factory, patientId, encounterId, defaultStartTime);
+		f.setObservations(facts);
+		process(f);
+	}
+	public void processEncounter(Patient patient, Visit visit, List<Observation> facts) throws ScriptException{
+		VisitExtensionFacts f = new VisitExtensionFacts(factory, patient, visit);
+		f.setObservations(facts);
+		process(f);
 	}
 }

histream-js/src/main/java/de/sekmi/histream/scripting/Fact.java

@@ -29,12 +29,12 @@ public class Fact {
 		return this;
 	}
 	
-	public Value value(String value){
+	public StringValue value(String value){
 		if( value == null ){
 			observation.setValue(null);
 			return null;
 		}
-		Value v = new StringValue(value);
+		StringValue v = new StringValue(value);
 		observation.setValue(v);
 		return v;
 	}
@@ -45,12 +45,12 @@ public class Fact {
 	 * @param value value
 	 * @return value object
 	 */
-	public Value value(Double value){
+	public NumericValue value(Double value){
 		if( value == null ){
 			observation.setValue(null);
 			return null;
 		}
-		Value v = new NumericValue(new BigDecimal(value));
+		NumericValue v = new NumericValue(new BigDecimal(value));
 		observation.setValue(v);
 		return v;
 	}

histream-js/src/main/java/de/sekmi/histream/scripting/SimpleFacts.java

+package de.sekmi.histream.scripting;
+
+import de.sekmi.histream.DateTimeAccuracy;
+import de.sekmi.histream.Observation;
+import de.sekmi.histream.ObservationFactory;
+
+/**
+ * Facts implementation which doesn't use
+ * any observation extensions.
+ * 
+ * @author R.W.Majeed
+ *
+ */
+public class SimpleFacts extends AbstractFacts {
+
+	// without extensions
+	private String patientId;
+	private String encounterId;
+	private DateTimeAccuracy defaultStartTime;
+
+
+	public SimpleFacts(ObservationFactory factory, String patientId, String encounterId, DateTimeAccuracy defaultStartTime){
+		super(factory);
+		this.patientId = patientId;
+		this.encounterId = encounterId;
+		this.defaultStartTime = defaultStartTime;
+	}
+
+	@Override
+	protected Observation create(String conceptId) {
+		Observation o = factory.createObservation(patientId, conceptId, defaultStartTime);
+		if( encounterId != null ){
+			o.setEncounterId(encounterId);
+		}
+		if( source != null ){
+			o.setSource(source);
+		}
+		return o;
+	}
+}

histream-js/src/main/java/de/sekmi/histream/scripting/VisitExtensionFacts.java

+package de.sekmi.histream.scripting;
+
+import java.util.Objects;
+
+import de.sekmi.histream.Observation;
+import de.sekmi.histream.ObservationFactory;
+import de.sekmi.histream.ext.Patient;
+import de.sekmi.histream.ext.Visit;
+
+public class VisitExtensionFacts extends AbstractFacts {
+	private Patient patient;
+	private Visit visit;
+	
+	public VisitExtensionFacts(ObservationFactory factory, Patient patient, Visit visit) {
+		super(factory);
+		Objects.requireNonNull(patient);
+		Objects.requireNonNull(visit);
+		this.patient = patient;
+		this.visit = visit;
+	}
+	
+	@Override
+	protected Observation create(String conceptId) {
+		Observation o = factory.createObservation(patient.getId(), conceptId, visit.getStartTime());
+		o.setExtension(Patient.class, patient);
+		o.setEncounterId(visit.getId());
+		o.setExtension(Visit.class, visit);
+		return o;
+	}
+
+}

histream-js/src/test/java/de/sekmi/histream/scripting/TestEncounterScriptEngine.java

 package de.sekmi.histream.scripting;
 
-import java.io.IOException;
-import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import javax.script.ScriptException;
 
 import org.junit.Assert;
 import org.junit.Test;
@@ -15,7 +12,8 @@ import de.sekmi.histream.DateTimeAccuracy;
 import de.sekmi.histream.Observation;
 import de.sekmi.histream.ObservationFactory;
 import de.sekmi.histream.Value;
-import de.sekmi.histream.ext.ExternalSourceType;
+import de.sekmi.histream.ext.Patient;
+import de.sekmi.histream.impl.CachedPatientExtension;
 import de.sekmi.histream.impl.ExternalSourceImpl;
 import de.sekmi.histream.impl.ObservationFactoryImpl;
 
@@ -37,9 +35,7 @@ public class TestEncounterScriptEngine {
 		EncounterScriptEngine e = new EncounterScriptEngine();
 		e.setObservationFactory(factory);
 		e.addScript(getClass().getResource("/postprocess-encounter-1.js"), "UTF-8", "script1");
-
 		// run
-		ExternalSourceType source = new ExternalSourceImpl("script", Instant.now());
 		e.processEncounter("P1", "E1", DateTimeAccuracy.parsePartialIso8601("2011-02-01"), list);
 
 		// verify
@@ -47,4 +43,42 @@ public class TestEncounterScriptEngine {
 		Assert.assertEquals("test1", last.getConceptId());
 		Assert.assertEquals(Value.Type.Numeric, last.getValue().getType());
 	}
+	
+	@Test
+	/**
+	 * Verifies that the non-extension script call for {@link AbstractFacts}
+	 * will work with extensions (if the patient extension is cached)
+	 * 
+	 * @throws Exception failure
+	 */
+	public void verifyPatientExtensionForNonExtensionCall() throws Exception{
+		ObservationFactory factory = new ObservationFactoryImpl();
+		// this test works only with CachedPatientExtension
+		factory.registerExtension(new CachedPatientExtension());
+		DateTimeAccuracy start = DateTimeAccuracy.parsePartialIso8601("2011");
+		// create full observation
+		Observation o = factory.createObservation("P1", "C1", start);
+		o.setSource(new ExternalSourceImpl());
+		Patient p = o.getExtension(Patient.class);
+		p.setGivenName("A");
+		p.setSurname("B");
+		p.setBirthDate(start);
+		// create list
+		List<Observation> list = new ArrayList<>();
+		list.add(o);
+		
+		// prepare engine
+		EncounterScriptEngine e = new EncounterScriptEngine();
+		e.setObservationFactory(factory);
+		e.addScript(getClass().getResource("/postprocess-encounter-1.js"), "UTF-8", "script1");
+		// run
+		e.processEncounter("P1", "C1", DateTimeAccuracy.parsePartialIso8601("2011-02-01"), list);
+		
+		Observation o2 = list.get(1);
+		Assert.assertNotEquals(o, o2);
+		Patient p2 = o2.getExtension(Patient.class);
+		Assert.assertNotNull(p2);
+		Assert.assertEquals(p, p2);
+		
+	}
 }

histream-js/src/test/java/de/sekmi/histream/scripting/TestFacts.java

@@ -45,7 +45,7 @@ public class TestFacts {
 	
 	@Test
 	public void verifyAddFacts() throws ScriptException{
-		Facts f = new Facts(factory, "P1", "V1", defaultStart);
+		SimpleFacts f = new SimpleFacts(factory, "P1", "V1", defaultStart);
 		f.setObservations(list);
 		engine.put("facts", f);
 		engine.eval("facts.add('C4')");
@@ -59,7 +59,7 @@ public class TestFacts {
 	
 	@Test
 	public void verifyHasFacts() throws ScriptException{
-		Facts f = new Facts(factory, "P1", "V1", defaultStart);
+		SimpleFacts f = new SimpleFacts(factory, "P1", "V1", defaultStart);
 		f.setObservations(list);
 		engine.put("facts", f);