histream-import/pom.xml

@@ -4,12 +4,12 @@
 
 	<groupId>de.sekmi.histream</groupId>
 	<artifactId>histream-import</artifactId>
-	<version>0.14-SNAPSHOT</version>
+	<version>0.16-SNAPSHOT</version>
 
 	<parent>
 		<groupId>de.sekmi.histream</groupId>
 		<artifactId>histream</artifactId>
-		<version>0.14-SNAPSHOT</version>
+		<version>0.16-SNAPSHOT</version>
 	</parent>
 	
 	<properties>
@@ -50,13 +50,13 @@
 		<dependency>
 			<groupId>de.sekmi.histream</groupId>
 			<artifactId>histream-core</artifactId>
-			<version>0.14-SNAPSHOT</version>
+			<version>0.16-SNAPSHOT</version>
 		</dependency>
 		<!-- script support -->
 		<dependency>
 			<groupId>de.sekmi.histream</groupId>
 			<artifactId>histream-js</artifactId>
-			<version>0.14-SNAPSHOT</version>
+			<version>0.16-SNAPSHOT</version>
 		</dependency>
 		<!-- add later for sorting data tables
 		<dependency>

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

@@ -14,6 +14,7 @@ import de.sekmi.histream.etl.config.DataSource;
 import de.sekmi.histream.etl.config.EavTable;
 import de.sekmi.histream.etl.config.Meta;
 import de.sekmi.histream.etl.config.WideTable;
+import de.sekmi.histream.etl.filter.FilterPostProcessingQueue;
 import de.sekmi.histream.impl.ObservationFactoryImpl;
 import de.sekmi.histream.impl.SimplePatientExtension;
 import de.sekmi.histream.impl.SimpleVisitExtension;
@@ -114,7 +115,7 @@ public class ETLObservationSupplier implements ObservationSupplier{
 	 * @throws ParseException configuration error
 	 */
 	public ETLObservationSupplier(DataSource ds, ObservationFactory factory) throws IOException, ParseException {
-		this(ds,factory,ds.createFactQueue(factory));
+		this(ds,factory,new FilterPostProcessingQueue(ds, factory));
 	}
 	/**
 	 * Construct a new observation supplier directly from a {@link DataSource}.

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

@@ -16,9 +16,7 @@ import javax.xml.bind.annotation.XmlElementWrapper;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlSeeAlso;
 
-import de.sekmi.histream.ObservationFactory;
-import de.sekmi.histream.etl.FactGroupingQueue;
-import de.sekmi.histream.etl.ScriptProcessingQueue;
+import de.sekmi.histream.etl.filter.PostProcessingFilter;
 
 /**
  * Data source configuration.
@@ -56,6 +54,8 @@ public class DataSource {
 	@XmlElement(name="eav-table")
 	EavTable[] eavTables;
 	
+	@XmlElement(name="post-processing", required=false)
+	PostProcessing postProcessing;
 	/**
 	 * Scripts to execute for each visit. A script
 	 * can add or delete facts for the visit. If scripts
@@ -111,6 +111,12 @@ public class DataSource {
 		return ds;
 	}
 
+	public PostProcessingFilter[] getPostProcessingFilters(){
+		if( postProcessing == null ){
+			return new PostProcessingFilter[]{};
+		}
+		return postProcessing.filter;
+	}
 	/**
 	 * If scripts are present, an instance of {@link ScriptProcessingQueue}
 	 * is returned. Otherwise an instance of {@link FactGroupingQueue}.
@@ -118,7 +124,7 @@ public class DataSource {
 	 * @return fact queue
 	 * @throws IOException error
 	 */
-	public FactGroupingQueue createFactQueue(ObservationFactory factory) throws IOException{
+//	public FactGroupingQueue createFactQueue(ObservationFactory factory) throws IOException{
 //		if( true ){
 //			// TODO debug problems with visitpostprocessorqueue
 //			return new VisitPostProcessorQueue() {
@@ -127,10 +133,10 @@ public class DataSource {
 //				}
 //			};
 //		}
-		if( scripts == null || scripts.length == 0 ){
-			return new FactGroupingQueue();
-		}else{
-			return new ScriptProcessingQueue(scripts, meta, factory);
-		}
-	}
+//		if( scripts == null || scripts.length == 0 ){
+//			return new FactGroupingQueue();
+//		}else{
+//			return new ScriptProcessingQueue(scripts, meta, factory);
+//		}
+//	}
 }

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

+package de.sekmi.histream.etl.config;
+
+import javax.xml.bind.annotation.XmlElement;
+
+import de.sekmi.histream.etl.filter.PostProcessingFilter;
+
+public class PostProcessing {
+	@XmlElement
+	PostProcessingFilter[] filter;
+
+}

histream-import/src/main/java/de/sekmi/histream/etl/filter/DuplicateFactFilter.java

+package de.sekmi.histream.etl.filter;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+import de.sekmi.histream.scripting.AbstractFacts;
+
+@XmlType(name="duplicate-fact")
+public class DuplicateFactFilter extends PostProcessingFilter{
+
+	@XmlElement
+	public String[] concept;
+
+	@Override
+	public void processVisit(AbstractFacts facts) {
+		// TODO Auto-generated method stub
+		
+	}
+
+}

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

-package de.sekmi.histream.etl;
+package de.sekmi.histream.etl.filter;
 
 import java.io.IOException;
-import java.io.Reader;
 import java.io.UncheckedIOException;
 
 import javax.script.ScriptException;
 
 import de.sekmi.histream.ObservationFactory;
-import de.sekmi.histream.etl.config.Meta;
-import de.sekmi.histream.etl.config.Script;
+import de.sekmi.histream.etl.VisitPostProcessorQueue;
+import de.sekmi.histream.etl.config.DataSource;
+import de.sekmi.histream.scripting.AbstractFacts;
 import de.sekmi.histream.scripting.EncounterScriptEngine;
 
-public class ScriptProcessingQueue extends VisitPostProcessorQueue {
+public class FilterPostProcessingQueue extends VisitPostProcessorQueue {
 	private EncounterScriptEngine engine;
+	private PostProcessingFilter[] filters;
 
-	public ScriptProcessingQueue(Script[] scripts, Meta meta, ObservationFactory factory) throws IOException {
+	public FilterPostProcessingQueue(DataSource ds, ObservationFactory factory) throws IOException {
 		try {
 			engine = new EncounterScriptEngine();
 		} catch (ScriptException e) {
@@ -22,25 +23,37 @@ public class ScriptProcessingQueue extends VisitPostProcessorQueue {
 		}
 		engine.setObservationFactory(factory);
 
-		// load scripts
-		for( int i=0; i<scripts.length; i++ ){
-			try( Reader r = scripts[i].openReader(meta) ){
-				engine.addScript(r, meta.getSourceId(), scripts[i].getTimestamp(meta));
-			} catch (ScriptException e) {
-				throw new IOException("Script error in script "+i, e);
+		filters = ds.getPostProcessingFilters();
+		// load script files into engine
+		for( int i=0; i<filters.length; i++ ){
+			if( filters[i] instanceof ScriptFilter ){
+				((ScriptFilter)filters[i]).loadIntoEngine(engine, ds.getMeta());
 			}
 		}
+
+		// load scripts
+//		for( int i=0; i<ds.length; i++ ){
+//			try( Reader r = scripts[i].openReader(meta) ){
+//				engine.addScript(r, meta.getSourceId(), scripts[i].getTimestamp(meta));
+//			} catch (ScriptException e) {
+//				throw new IOException("Script error in script "+i, e);
+//			}
+//		}
 	}
 	@Override
 	protected void postProcessVisit() {
 		if( getVisit() == null ){
 			return; // don't want null visits
 		}
-		try {
-			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);
+		AbstractFacts facts = engine.wrapEncounterFacts(getPatient(), getVisit(), getVisitFacts());
+		
+		for( int i=0; i<filters.length; i++ ){
+			try {
+				filters[i].processVisit(facts);
+			} catch (IOException e) {
+				// TODO UncheckedIOException might be unwrapped and message might be lost, verify this
+				throw new UncheckedIOException("Filter execution failed for patient="+getPatient().getId()+", visit="+getVisit().getId(), e);
+			}
 		}
 	}
 	

histream-import/src/main/java/de/sekmi/histream/etl/filter/PostProcessingFilter.java

+package de.sekmi.histream.etl.filter;
+
+import java.io.IOException;
+
+import javax.xml.bind.annotation.XmlSeeAlso;
+
+import de.sekmi.histream.scripting.AbstractFacts;
+
+@XmlSeeAlso({DuplicateFactFilter.class, ScriptFilter.class})
+public abstract class PostProcessingFilter {
+
+	public abstract void processVisit(AbstractFacts facts)throws IOException;
+}

histream-import/src/main/java/de/sekmi/histream/etl/filter/ScriptFilter.java

+package de.sekmi.histream.etl.filter;
+
+
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.URL;
+import java.time.Instant;
+
+import javax.script.ScriptException;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlTransient;
+import javax.xml.bind.annotation.XmlType;
+
+import de.sekmi.histream.etl.config.Meta;
+import de.sekmi.histream.scripting.AbstractFacts;
+import de.sekmi.histream.scripting.EncounterScriptEngine;
+
+@XmlType(name="javascript")
+public class ScriptFilter extends PostProcessingFilter{
+
+	/** 
+	 * Character encoding for an external script file 
+	 */
+	@XmlAttribute
+	String charset;
+	
+
+	/**
+	 * Specifies the URL of an external script file. The URL can be relative
+	 * to the configuration.
+	 */
+	@XmlAttribute
+	String src;
+	
+	/**
+	 * Literal script source
+	 */
+	@XmlElement
+	String script;
+
+
+	@XmlTransient
+	private int loadedIndex;
+	@XmlTransient
+	private EncounterScriptEngine engine;
+
+	public Reader openReader(Meta meta) throws IOException{
+		if( script != null ){
+			return new StringReader(script);
+		}else if( src != null ){
+			URL url = new URL(meta.getLocation(), src);
+			return new InputStreamReader(url.openStream(), this.charset);
+		}else{
+			return null;
+		}
+	}
+	
+	public Instant getTimestamp(Meta meta) throws IOException{
+		// TODO use last modified of external script files
+		return Instant.ofEpochMilli(meta.getLastModified());
+	}
+	public void loadIntoEngine(EncounterScriptEngine engine, Meta meta) throws IOException{
+		this.engine = engine;
+		try( Reader r = openReader(meta) ){
+			this.loadedIndex = engine.addScript(r, meta.getSourceId(), getTimestamp(meta));
+		} catch (ScriptException e) {
+			throw new IOException("Script error in filter[type=javascript]", e);
+		}
+		
+	}
+
+	@Override
+	public void processVisit(AbstractFacts facts) throws IOException {
+		try {
+			engine.processSingle(facts, loadedIndex);
+		} catch (ScriptException e) {
+			throw new IOException("Script execution failed", e);
+		}
+	}
+
+
+}

histream-import/src/main/java/de/sekmi/histream/etl/validation/Validator.java

@@ -75,6 +75,10 @@ public class Validator extends AbstractObservationHandler implements Transformat
 
 			// clear concepts
 			concepts.clear();
+			// add concept
+			if( duplicateConceptCheck ){
+				concepts.add(new StartPlusConcept(t));
+			}
 			
 			prevPatient = patid; // remember patient to suppress errors for the same patient
 

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

@@ -62,11 +62,11 @@ public class TestETLSupplier {
 		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());
+//		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{
@@ -141,5 +141,27 @@ public class TestETLSupplier {
 			System.out.println("Natrium-start: "+o.getStartTime());
 		}
 	}
+	@Test
+	public void verifyInlineScriptExecution() throws IOException, java.text.ParseException{
+		List<Observation> all = new ArrayList<>();
+		
+		os.stream().filter( o -> o.getConceptId().equals("cnt") ).forEach(all::add);
+//		for( Observation o : all ){
+//			System.out.println("cnt: "+o.getStartTime()+", "+o.getValue().getStringValue());
+//		}
+		// should have a cnt fact for each visit
+		Assert.assertEquals(4, all.size());
+	}
+	@Test
+	public void verifyExternalScriptExecution() throws IOException, java.text.ParseException{
+		List<Observation> all = new ArrayList<>();
+		
+		os.stream().filter( o -> o.getConceptId().equals("ext-js") ).forEach(all::add);
+//		for( Observation o : all ){
+//			System.out.println("cnt: "+o.getStartTime()+", "+o.getValue().getStringValue());
+//		}
+		// should have a cnt fact for each visit
+		Assert.assertEquals(4, all.size());
+	}
 
 }

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

@@ -12,6 +12,8 @@ import org.junit.Assert;
 import org.junit.Test;
 
 import de.sekmi.histream.etl.config.DataSource;
+import de.sekmi.histream.etl.filter.DuplicateFactFilter;
+import de.sekmi.histream.etl.filter.ScriptFilter;
 
 public class TestMarshall {
 
@@ -65,6 +67,13 @@ public class TestMarshall {
 			Assert.assertNotNull(ds.eavTables[0].virtualColumnMap);
 			Assert.assertNotNull(ds.eavTables[0].virtualColumnMap.get("f_eav_x"));
 			
+			// check post processing
+			Assert.assertNotNull(ds.postProcessing);
+			Assert.assertEquals(3, ds.postProcessing.filter.length);
+			Assert.assertEquals(DuplicateFactFilter.class, ds.postProcessing.filter[0].getClass());
+			DuplicateFactFilter f = (DuplicateFactFilter)ds.postProcessing.filter[0];
+			ScriptFilter sf = (ScriptFilter)ds.postProcessing.filter[1];
+			
 			// check script
 			/* Assert.assertEquals(2,  ds.scripts.length);
 			Assert.assertNull(ds.scripts[0].src);

histream-import/src/test/java/de/sekmi/histream/etl/validation/TestValidator.java

@@ -51,4 +51,22 @@ public class TestValidator {
 			Streams.transfer(os, v);
 		}
 	}
+	@Test
+	public void validateData4() throws Exception{
+		// duplicate concepts
+		try( ObservationSupplier os = ETLObservationSupplier.load(getClass().getResource("/data/test-4-datasource.xml")) ){
+			Validator v = new Validator(true,true);
+			v.setErrorHandler(e -> {throw new RuntimeException(e);});
+			Streams.transfer(os, v);
+		}catch( RuntimeException e ){
+			if( e.getCause() instanceof DuplicateConceptException ){
+				// expected behaviour
+				return;
+			}else{
+				// unexpected exceptoin
+				throw e;
+			}
+		}
+		Assert.fail("Exception expected");
+	}
 }

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

@@ -35,7 +35,6 @@
 	<visit-table>
 		<source xsi:type="csv-file">
 			<url>test-1-visits.txt</url>
-			<type>text/csv</type>
 			<separator>\t</separator>
 		</source>
 		<idat>
@@ -139,13 +138,18 @@
 		<ignore column="user" xsi:type="string"/>
 	</eav-table>
 	<!-- scripts are run for each complete encounter in the order of occurrence -->
-	<script type="text/javascript"><![CDATA[
-		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"/>
+	<post-processing>
+		<filter xsi:type="duplicate-fact">
+			<concept>kalium</concept>
+		</filter>
+		<filter xsi:type="javascript">
+			<script><![CDATA[
+			if( facts.get("natrium") && facts.get("kalium") ){
+				facts.add("nakl").value(1);
+			}
+			facts.add("cnt").value(facts.size());
+		]]></script>
+		</filter>
+		<filter xsi:type="javascript" charset="UTF-8" src="test-1-script.js"/>
+	</post-processing>
 </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(7);
+facts.add("ext-js").value(24);

histream-import/src/test/resources/data/test-2-datasource.xml

@@ -35,7 +35,6 @@
 	<visit-table>
 		<source xsi:type="csv-file">
 			<url>test-2-visits-duplicate.txt</url>
-			<type>text/csv</type>
 			<separator>\t</separator>
 		</source>
 		<idat>

histream-import/src/test/resources/data/test-3-datasource.xml

@@ -35,7 +35,6 @@
 	<visit-table>
 		<source xsi:type="csv-file">
 			<url>test-3-visits-empty.txt</url>
-			<type>text/csv</type>
 			<separator>\t</separator>
 		</source>
 		<idat>

histream-import/src/test/resources/data/test-4-datasource.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<datasource version="1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+	<!-- Duplicate concept for patient -->
+	<meta>
+		<id>LTx_PH_ILD_COPD</id>
+		<etl-strategy>replace-source</etl-strategy>
+	</meta>
+	
+	 <patient-table>
+		<source xsi:type="csv-file">
+			<url>test-4-table.csv</url>
+			<separator>;</separator>
+		</source>
+		<idat>
+      <!-- Vorname, Nachname, Geschlecht unbekannt -->
+			<patient-id column="Pheno-ID"/>
+			<given-name column="Pheno-ID"/>
+			<surname column="Pheno-ID"/>
+		</idat>
+		<ignore xsi:type="string" column="*"/>
+	</patient-table>
+	<visit-table>
+		<source xsi:type="csv-file">
+			<url>test-4-table.csv</url>
+			<separator>;</separator>
+		</source>
+		<idat>
+			<patient-id column="Pheno-ID"/>
+			<visit-id column="Zeitpunkt"/>
+			<start column="Zeitpunkt" format="d.M.u[ H[:m[:s]]]"/>
+		</idat>
+	<ignore xsi:type="string" column="*"/>
+	</visit-table>
+	<eav-table>
+		<source xsi:type="csv-file">
+			<url>test-4-table.csv</url>
+			<separator>;</separator>
+		</source>	
+		<idat>
+			<patient-id column="Pheno-ID"/>
+			<visit-id column="Zeitpunkt"/>
+		</idat>
+		<mdat>
+			<concept column="Export-Param"/>
+			<start column="Zeitpunkt" format="d.M.u[ H[:m[:s]]]"/>
+			<end column="Zeitpunkt" format="d.M.u[ H[:m[:s]]]"/>
+			<type constant-value="string"/>
+			<value column="Wert" na=""/>
+			<unit column="Einheiten" na=""/>
+		</mdat>
+		<virtual>
+			<value column="Diagnose" xsi:type="string" na="">
+				<map>					
+					<otherwise log-warning="Unexpected value" action="drop-fact" />
+				</map>
+			</value>
+			<value column="Zusatzdiagnose" xsi:type="string" na="">
+				<map>
+					<case value="IPF" set-concept="B:DP-ID-IPF" set-value=""/>
+					<case value="UIP" set-concept="B:DP-ID-IPF" set-value=""/>
+					<otherwise log-warning="Unexpected value" action="drop-fact" />
+				</map>
+			</value>
+			<value column="Probenart" xsi:type="string" na="">
+				<map>
+					<otherwise action="drop-fact"/>
+				</map>
+			</value>
+			<value column="Diesease Area" xsi:type="string" na="">
+				<map>
+					<otherwise action="drop-fact"/>
+				</map>
+			</value>
+		</virtual>	
+		<ignore xsi:type="string" column="*"/>
+	</eav-table>
+</datasource>

histream-import/src/test/resources/data/test-4-table.csv

+Pheno-ID;Bereich;Zeitpunkt;Export-Param;Wert;Einheiten;
+Mmqp212;Biobank-IDs;21.04.2016;Zusatzdiagnose;UIP;;
+Mmqp212;Biobank-IDs;21.04.2016;Zusatzdiagnose;IPF;;
\ No newline at end of file

histream-js/pom.xml

@@ -4,12 +4,12 @@
 
 	<groupId>de.sekmi.histream</groupId>
 	<artifactId>histream-js</artifactId>
-	<version>0.14-SNAPSHOT</version>
+	<version>0.16-SNAPSHOT</version>
 
 	<parent>
 		<groupId>de.sekmi.histream</groupId>
 		<artifactId>histream</artifactId>
-		<version>0.14-SNAPSHOT</version>
+		<version>0.16-SNAPSHOT</version>
 	</parent>
   
 	<build>

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

@@ -54,21 +54,25 @@ public class EncounterScriptEngine {
 		scripts = new LinkedList<>();
 	}
 
-	public void addScript(String script, String sourceId, Instant timestamp) throws ScriptException{
+	public int addScript(String script, String sourceId, Instant timestamp) throws ScriptException{
+		int index = scripts.size();
 		scripts.add(new Script(((Compilable)engine).compile(script), sourceId, timestamp));
+		return index;
 	}
-	public void addScript(URL location, String charset, String sourceId) throws ScriptException, IOException{
+	public int addScript(URL location, String charset, String sourceId) throws ScriptException, IOException{
 		URLConnection conn = location.openConnection();
 		Instant timestamp = Instant.ofEpochMilli(conn.getLastModified());
 		try(
 				InputStream in = conn.getInputStream();
 				Reader reader = new InputStreamReader(in, charset)
 		){
-			addScript(reader, sourceId, timestamp);
+			return addScript(reader, sourceId, timestamp);
 		}
 	}
-	public void addScript(Reader reader, String sourceId, Instant timestamp) throws ScriptException{
+	public int addScript(Reader reader, String sourceId, Instant timestamp) throws ScriptException{
+		int index = scripts.size();
 		scripts.add(new Script(((Compilable)engine).compile(reader), sourceId, timestamp));	
+		return index;
 	}
 	
 	public int getScriptCount(){
@@ -78,7 +82,7 @@ public class EncounterScriptEngine {
 	public void setObservationFactory(ObservationFactory factory){
 		this.factory = factory;
 	}
-	private void process(AbstractFacts facts) throws ScriptException{
+	public void processAll(AbstractFacts facts) throws ScriptException{
 		Bindings b = engine.createBindings();
 		b.put("facts", facts);
 		for( Script script : scripts ){
@@ -87,14 +91,28 @@ public class EncounterScriptEngine {
 		}
 		// 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{
+	public void processSingle(AbstractFacts facts, int scriptIndex) throws ScriptException{
+		Bindings b = engine.createBindings();
+		b.put("facts", facts);
+		
+		Script script = scripts.get(scriptIndex);
+		facts.setSource(script.source);
+		script.script.eval(b);
+	}
+	
+	public AbstractFacts wrapEncounterFacts(String patientId, String encounterId, DateTimeAccuracy defaultStartTime, List<Observation> facts){
 		SimpleFacts f = new SimpleFacts(factory, patientId, encounterId, defaultStartTime);
 		f.setObservations(facts);
-		process(f);
+		return f;
 	}
-	public void processEncounter(Patient patient, Visit visit, List<Observation> facts) throws ScriptException{
+	public AbstractFacts wrapEncounterFacts(Patient patient, Visit visit, List<Observation> facts){
 		VisitExtensionFacts f = new VisitExtensionFacts(factory, patient, visit);
 		f.setObservations(facts);
-		process(f);
+		return f;
+	}
+	// TODO add method to execute a single script
+
+	public void processEncounter(String patientId, String encounterId, DateTimeAccuracy defaultStartTime, List<Observation> facts) throws ScriptException {
+		processAll( wrapEncounterFacts(patientId, encounterId, defaultStartTime, facts) );
 	}
 }

pom.xml

@@ -55,10 +55,10 @@
 		<module>histream-i2b2</module>
 		<module>histream-core</module>
 		<module>histream-export</module>
+		<module>histream-js</module>
+		<module>histream-import</module>
 		<!--
 		<module>histream-skos</module>
-		<module>histream-import</module>
-		<module>histream-js</module>
 		<module>histream-maven-plugin</module> -->
 		<!--
 		<module>i2b2-integration-tests</module>