Commit dc7f8635 authored by R.W.Majeed's avatar R.W.Majeed

fixed and improved javascript execution

parent ec55c7c0
......@@ -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}.
*
......
......@@ -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();
}
}
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{
......
......@@ -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
......
......@@ -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>
// 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
......@@ -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;
}
}
......@@ -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);
}
}
......@@ -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;
}
......
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;
}
}
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;
}
}
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);
}
}
......@@ -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);
......
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