javascript integration for histream-import, still bugs in VisitPostProcessorQueue (58551eac) · Commits · Raphael Majeed / histream

histream-import/pom.xml

+6 −0

Original line number	Diff line number	Diff line
		@@ -52,6 +52,12 @@
		<artifactId>histream-core</artifactId>
		<version>0.8-SNAPSHOT</version>
		</dependency>
		<!-- script support -->
		<dependency>
		<groupId>de.sekmi.histream</groupId>
		<artifactId>histream-js</artifactId>
		<version>0.8-SNAPSHOT</version>
		</dependency>
		<!-- add later for sorting data tables
		<dependency>
		<groupId>com.google.protobuf</groupId>

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

+2 −6

Original line number	Diff line number	Diff line
		@@ -7,16 +7,12 @@ import java.util.ArrayList;
		import java.util.Iterator;
		import java.util.List;

		import javax.xml.bind.JAXB;

		import de.sekmi.histream.Observation;
		import de.sekmi.histream.ObservationFactory;
		import de.sekmi.histream.ObservationSupplier;
		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.PatientTable;
		import de.sekmi.histream.etl.config.VisitTable;
		import de.sekmi.histream.etl.config.WideTable;
		import de.sekmi.histream.impl.ObservationFactoryImpl;
		import de.sekmi.histream.impl.SimplePatientExtension;
		@@ -112,7 +108,7 @@ public class ETLObservationSupplier implements ObservationSupplier{
		* @throws ParseException configuration error
		*/
		public ETLObservationSupplier(DataSource ds, ObservationFactory factory) throws IOException, ParseException {
		this(ds,factory,new FactGroupingQueue());
		this(ds,factory,ds.createFactQueue(factory));
		}
		/**
		* Construct a new observation supplier directly from a {@link DataSource}.
		@@ -123,7 +119,7 @@ public class ETLObservationSupplier implements ObservationSupplier{
		* @throws IOException error reading configuration or table data
		* @throws ParseException configuration error
		*/
		public ETLObservationSupplier(DataSource ds, ObservationFactory factory, FactGroupingQueue queue) throws IOException, ParseException {
		protected ETLObservationSupplier(DataSource ds, ObservationFactory factory, FactGroupingQueue queue) throws IOException, ParseException {
		this.ds = ds;
		this.sync = new ExtensionSync(factory);
		this.queue = queue;

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

0 → 100644

+47 −0

Original line number	Diff line number	Diff line
		package de.sekmi.histream.etl;

		import java.io.IOException;
		import java.io.Reader;
		import java.io.UncheckedIOException;
		import java.net.URL;

		import javax.script.ScriptException;

		import de.sekmi.histream.ObservationFactory;
		import de.sekmi.histream.etl.config.Script;
		import de.sekmi.histream.scripting.EncounterScriptEngine;

		public class ScriptProcessingQueue extends VisitPostProcessorQueue {
		private EncounterScriptEngine engine;

		public ScriptProcessingQueue(Script[] scripts, URL baseURL, ObservationFactory factory) throws IOException {
		try {
		engine = new EncounterScriptEngine();
		} catch (ScriptException e) {
		throw new IOException("Unable to create script engine", e);
		}
		engine.setObservationFactory(factory);

		// load scripts
		for( int i=0; i<scripts.length; i++ ){
		try( Reader r = scripts[i].openReader(baseURL) ){
		engine.addScript(r);
		} 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().getId(), getVisit().getId(), getVisit().getStartTime(), getVisitFacts());
		} catch (ScriptException e) {
		IOException io = new IOException("Error during script execution for patient="+getPatient().getId()+", visit="+getVisit().getId(), e);
		throw new UncheckedIOException(io);
		}
		}

		}

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

+2 −1

Original line number	Diff line number	Diff line
		@@ -75,7 +75,8 @@ public abstract class VisitPostProcessorQueue extends FactGroupingQueue {
		// next fact
		nextFact = super.get();
		}

		// TODO visit can be processed, without having any facts left to return (either there were no facts in the visit or or postProcessing removed all facts)
		// TODO maybe rename visitProcessed to visitProcessedNonempty
		if( visitProcessed ){
		if( !visitFacts.isEmpty() ){
		// remove first

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

+30 −0

Original line number	Diff line number	Diff line
		package de.sekmi.histream.etl.config;

		import java.io.IOException;
		import java.net.URL;
		import java.util.Arrays;
		import java.util.List;

		import javax.script.ScriptException;
		import javax.xml.bind.JAXB;
		import javax.xml.bind.annotation.XmlAccessType;
		import javax.xml.bind.annotation.XmlAccessorType;
		@@ -12,6 +14,11 @@ 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.VisitPostProcessorQueue;

		/**
		* Data source configuration.
		* This is the XML root element which can be loaded
		@@ -88,4 +95,27 @@ public class DataSource {
		ds.getMeta().setLocation(configuration);
		return ds;
		}

		/**
		* If scripts are present, an instance of {@link ScriptProcessingQueue}
		* is returned. Otherwise an instance of {@link FactGroupingQueue}.
		* @return fact queue
		* @throws IOException
		* @throws
		*/
		public FactGroupingQueue createFactQueue(ObservationFactory factory) throws IOException{
		// if( true ){
		// // TODO debug problems with visitpostprocessorqueue
		// return new VisitPostProcessorQueue() {
		// @Override
		// protected void postProcessVisit() {
		// }
		// };
		// }
		if( true \|\| scripts == null \|\| scripts.length == 0 ){
		return new FactGroupingQueue();
		}else{
		return new ScriptProcessingQueue(scripts, meta.getLocation(), factory);
		}
		}
		}