date parsing will throw checked ParseException

histream-core/src/main/java/de/sekmi/histream/DateTimeAccuracy.java

 package de.sekmi.histream;
 
+import java.text.ParseException;
 import java.time.DateTimeException;
 
 /*
@@ -194,14 +195,16 @@ public class DateTimeAccuracy implements Temporal, Comparable<DateTimeAccuracy>
 	 * @return date time with accuracy as derived from parse
 	 * @throws IllegalArgumentException for unparsable string
 	 */
-	public static DateTimeAccuracy parsePartialIso8601(String str)throws IllegalArgumentException{
-		if( str.length() < 4 )throw new IllegalArgumentException("Need at least 4 characters for year: "+str);
+	public static DateTimeAccuracy parsePartialIso8601(String str)throws ParseException{
+		if( str.length() < 4 )throw new ParseException("Need at least 4 characters for year: "+str, str.length());
 		// parse year
 		int year = Integer.parseInt(str.substring(0, 4));
 		if( str.length() == 4 ){ // specified to accuracy of years
 			return new DateTimeAccuracy(year);
-		}else if( str.length() < 7 || str.charAt(4) != '-' ){
-			throw new IllegalArgumentException("Expected YYYY-MM");
+		}else if( str.length() < 7 ){
+			throw new ParseException("Expected YYYY-MM", str.length());
+		}else if( str.charAt(4) != '-' ){
+			throw new ParseException("Expected YYYY-MM", 4);
 		}
 		// parse month
 		int month = Integer.parseInt(str.substring(5, 7));

histream-core/src/main/java/de/sekmi/histream/io/FlatObservationSupplier.java

@@ -27,6 +27,7 @@ import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.UncheckedIOException;
 import java.math.BigDecimal;
+import java.text.ParseException;
 import java.time.LocalDateTime;
 import java.time.ZoneId;
 import java.util.Hashtable;
@@ -253,7 +254,7 @@ public class FlatObservationSupplier extends AbstractObservationParser implement
 			currentVisit = visitAccessor.accessStatic(visitId,currentPatient,(ExternalSourceType)this);
 		}
 	}
-	private void specialFields(SpecialConcept special, Record record){		
+	private void specialFields(SpecialConcept special, Record record) throws ParseException{		
 		// make sure current patient is valid
 		lazyCreatePatient(record.getPatID());
 		
@@ -325,7 +326,7 @@ public class FlatObservationSupplier extends AbstractObservationParser implement
 		return value;
 	}
 	
-	private void newObservation(Record record){
+	private void newObservation(Record record) throws ParseException{
 		DateTimeAccuracy ts;
 		DateTimeAccuracy sourceTs = getSourceDateTime();
 		if( record.getStartDate() == null ){
@@ -413,28 +414,33 @@ public class FlatObservationSupplier extends AbstractObservationParser implement
 				// continue;
 			}else{
 				// parse observation
-				Record fields = new Record(fieldSeparatorPattern.split(line, maxFields));
-				// fields: 0 patid, 1 encounter, 2 concept, 3: type, 4: value, 5: starttime, 
-				
-				// handle special concepts (defined by previous commands)
-				SpecialConcept special = specialConcepts.get(fields.getConcept());
-				if( special != null ){
-					specialFields(special, fields);
-					// continue;
-				}else if( inGroup ){
-					// first item is fact, following items are modifiers
-					if( fact == null ){
-						newObservation(fields);
+				try{
+					Record fields = new Record(fieldSeparatorPattern.split(line, maxFields));
+					// fields: 0 patid, 1 encounter, 2 concept, 3: type, 4: value, 5: starttime, 
+					
+					// handle special concepts (defined by previous commands)
+					SpecialConcept special = specialConcepts.get(fields.getConcept());
+					if( special != null ){
+						specialFields(special, fields);
+						// continue;
+					}else if( inGroup ){
+						// first item is fact, following items are modifiers
+						if( fact == null ){
+							newObservation(fields);
+						}else{
+							appendModifier(fields);
+						}
+						// continue;
+						// group ends with #@group(end)
 					}else{
-						appendModifier(fields);
+						// assert( fact == null )
+						newObservation(fields);
+						break;
 					}
-					// continue;
-					// group ends with #@group(end)
-				}else{
-					// assert( fact == null )
-					newObservation(fields);
-					break;
+				} catch (ParseException e) {
+					throw new UncheckedIOException(new IOException(e));
 				}
+
 			}
 		}while( true );
 		Observation ret = fact;

histream-core/src/main/java/de/sekmi/histream/io/GroupedXMLReader.java

@@ -3,6 +3,7 @@ package de.sekmi.histream.io;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.UncheckedIOException;
+import java.text.ParseException;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -146,16 +147,29 @@ public class GroupedXMLReader  implements ObservationSupplier {
 		
 		// register with extension
 		currentPatient = patientAccessor.accessStatic(patientId, (ExternalSourceType)es);
+		// immediately set source timestamp
+		if( es != null ){
+			currentPatient.setSourceTimestamp(es.getSourceTimestamp());
+		}
 		// TODO set patient data
 		if( patientData.containsKey("birthdate") ){
-			currentPatient.setBirthDate(DateTimeAccuracy.parsePartialIso8601(patientData.get("birthdate")));
+			String dob = patientData.get("birthdate");
+			try {
+				currentPatient.setBirthDate(DateTimeAccuracy.parsePartialIso8601(dob));
+			} catch (ParseException e) {
+				throw new XMLStreamException("Unable to parse birthdate: "+dob, reader.getLocation(), e);
+			}
 		}
 		if( patientData.containsKey("deceased") ){
 			// patient known to be deceased
 			currentPatient.setDeceased(true);
 			String date = patientData.get("deceased");
 			if( date != null ){
-				currentPatient.setDeathDate(DateTimeAccuracy.parsePartialIso8601(date));
+				try {
+					currentPatient.setDeathDate(DateTimeAccuracy.parsePartialIso8601(date));
+				} catch (ParseException e) {
+					throw new XMLStreamException("Unable to parse deceased date: "+date, reader.getLocation(), e);
+				}
 			}
 		}
 		if( patientData.containsKey("gender") ){
@@ -167,9 +181,6 @@ public class GroupedXMLReader  implements ObservationSupplier {
 		if( patientData.containsKey("given-name") ){
 			currentPatient.setGivenName(patientData.get("given-name"));
 		}
-		if( es != null ){
-			currentPatient.setSourceTimestamp(es.getSourceTimestamp());
-		}
 		
 	}
 	
@@ -224,12 +235,22 @@ public class GroupedXMLReader  implements ObservationSupplier {
 			reader.nextTag();
 		}
 		if( visitData.containsKey("start") ){
-			encounterStart = DateTimeAccuracy.parsePartialIso8601(visitData.get("start"));
+			String date = visitData.get("start");
+			try {
+				encounterStart = DateTimeAccuracy.parsePartialIso8601(date);
+			} catch (ParseException e) {
+				throw new XMLStreamException("Unable to parse encounter/start: "+date, reader.getLocation(), e);
+			}
 		}else{
 			encounterStart = null;
 		}
 		if( visitData.containsKey("end") ){
-			encounterEnd = DateTimeAccuracy.parsePartialIso8601(visitData.get("end"));
+			String date = visitData.get("end");
+			try {
+				encounterEnd = DateTimeAccuracy.parsePartialIso8601(date);
+			} catch (ParseException e) {
+				throw new XMLStreamException("Unable to parse encounter/end: "+date, reader.getLocation(), e);
+			}
 		}else{
 			encounterEnd = null;
 		}

histream-core/src/main/java/de/sekmi/histream/io/XMLObservationParser.java

@@ -22,6 +22,7 @@ package de.sekmi.histream.io;
 
 
 import java.math.BigDecimal;
+import java.text.ParseException;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.logging.Logger;
@@ -104,7 +105,7 @@ class XMLObservationParser extends AbstractObservationParser{
 			// TODO: log error
 		}				
 	}
-	protected void newObservation(AttributeAccessor atts){
+	protected void newObservation(AttributeAccessor atts) throws ParseException{
 		// determine start time
 		DateTimeAccuracy start;
 		String ts = atts.getValue("start");
@@ -213,7 +214,7 @@ class XMLObservationParser extends AbstractObservationParser{
 		setMeta(ObservationSupplier.META_SOURCE_TIMESTAMP, atts.getValue("timestamp"));
 		setMeta(ObservationSupplier.META_SOURCE_ID, atts.getValue("id"));
 	}
-	protected void parseEncounter(AttributeAccessor atts){
+	protected void parseEncounter(AttributeAccessor atts) throws ParseException{
 		encounterStart = DateTimeAccuracy.parsePartialIso8601(atts.getValue("start"));
 		if( atts.getValue("end") != null ){
 			encounterEnd = DateTimeAccuracy.parsePartialIso8601(atts.getValue("end"));

histream-core/src/main/java/de/sekmi/histream/io/XMLObservationSupplier.java

@@ -24,6 +24,7 @@ package de.sekmi.histream.io;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.UncheckedIOException;
+import java.text.ParseException;
 
 import javax.xml.stream.FactoryConfigurationError;
 import javax.xml.stream.XMLInputFactory;
@@ -118,7 +119,11 @@ public class XMLObservationSupplier extends XMLObservationParser implements Obse
 			// read visit attributes
 
 			if( reader.getLocalName().equals("encounter") ){
-				parseEncounter(atts);
+				try {
+					parseEncounter(atts);
+				} catch (ParseException e) {
+					throw new XMLStreamException("Unable to parse encounter", reader.getLocation(), e);
+				}
 			}
 
 			String text = reader.getElementText();
@@ -158,7 +163,11 @@ public class XMLObservationSupplier extends XMLObservationParser implements Obse
 				|| reader.getLocalName().equals("eav-group")) ){
 			throw new XMLStreamException("Element eav-item or eav-group expected instead of "+reader.getLocalName(), reader.getLocation());
 		}
-		newObservation(atts);
+		try {
+			newObservation(atts);
+		} catch (ParseException e) {
+			throw new XMLStreamException("Unable to parse observation", reader.getLocation(), e);
+		}
 		if( reader.getLocalName().equals("eav-group") ){
 			// group item can have value
 			parseValueAttributes(atts);

histream-core/src/main/java/de/sekmi/histream/xml/DateTimeAccuracyAdapter.java

 package de.sekmi.histream.xml;
 
+import java.text.ParseException;
+
 import javax.xml.bind.annotation.adapters.XmlAdapter;
 
 import de.sekmi.histream.DateTimeAccuracy;
@@ -13,7 +15,7 @@ import de.sekmi.histream.DateTimeAccuracy;
 public class DateTimeAccuracyAdapter extends XmlAdapter<String, DateTimeAccuracy>{
 
 	@Override
-	public DateTimeAccuracy unmarshal(String v) {
+	public DateTimeAccuracy unmarshal(String v) throws ParseException {
 		if( v == null )return null;
 		return DateTimeAccuracy.parsePartialIso8601(v);
 	}

histream-core/src/test/java/de/sekmi/histream/impl/TestDateTimeAccuracy.java

 package de.sekmi.histream.impl;
 
+import java.text.ParseException;
+
 /*
  * #%L
  * histream
@@ -40,7 +42,7 @@ public class TestDateTimeAccuracy {
 		}
 	}
 	@Test
-	public void testParseToString(){
+	public void testParseToString() throws ParseException{
 		final String[] str = new String[]{"2001-03-04T10:16:07", "2001-03-04T10:16:00"};
 		DateTimeAccuracy a = DateTimeAccuracy.parsePartialIso8601(str[0]);
 		Assert.assertEquals(ChronoUnit.SECONDS, a.getAccuracy());
@@ -52,7 +54,7 @@ public class TestDateTimeAccuracy {
 	}
 	
 	@Test
-	public void testPartialDates(){
+	public void testPartialDates() throws ParseException{
 		final String[] str = {"2001-03-04T05:06","2001-03-04T05","2001-03-04","2001-03","2001"};
 		final ChronoUnit[] expectedAccuracy = {ChronoUnit.MINUTES, ChronoUnit.HOURS, ChronoUnit.DAYS, ChronoUnit.MONTHS, ChronoUnit.YEARS};
 		for( int i=0; i<expectedAccuracy.length; i++ ){

histream-core/src/test/java/de/sekmi/histream/io/FileObservationProviderTest.java

@@ -24,11 +24,13 @@ package de.sekmi.histream.io;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.UncheckedIOException;
 import java.time.temporal.ChronoField;
 import java.time.temporal.ChronoUnit;
 import java.util.Iterator;
 import java.util.function.Supplier;
 import java.math.BigDecimal;
+import java.text.ParseException;
 
 import javax.xml.bind.JAXBException;
 import javax.xml.stream.FactoryConfigurationError;
@@ -81,8 +83,12 @@ public class FileObservationProviderTest {
 				Assert.assertNotNull("Patient extension required", p);
 				Assert.assertEquals("XX12345", p.getId());
 				Assert.assertEquals(Boolean.TRUE, p.getDeceased());
-				Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2001-01-01"), p.getBirthDate());
-				Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2020"), p.getDeathDate());
+				try {
+					Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2001-01-01"), p.getBirthDate());
+					Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2020"), p.getDeathDate());
+				} catch (ParseException e) {
+					throw new RuntimeException(e);
+				}
 				Assert.assertEquals(Sex.female, p.getSex());
 				Assert.assertEquals("A B", p.getGivenName());
 				Assert.assertEquals("Dampf", p.getSurname());
@@ -93,8 +99,12 @@ public class FileObservationProviderTest {
 				Visit v = o.getExtension(Visit.class);
 				Assert.assertNotNull("Visit extension required", v);
 				Assert.assertEquals("Zuhause", v.getLocationId());
-				Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2014-01-01T10:30:00"), v.getStartTime());
-				Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2014-01-05T10:30:00"), v.getEndTime());
+				try{
+					Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2014-01-01T10:30:00"), v.getStartTime());
+					Assert.assertEquals(DateTimeAccuracy.parsePartialIso8601("2014-01-05T10:30:00"), v.getEndTime());
+				} catch (ParseException e) {
+					throw new RuntimeException(e);
+				}
 				// TODO test visit information
 				
 				// test source

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

@@ -3,7 +3,6 @@ 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;
 

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

@@ -7,7 +7,6 @@ import java.net.URLConnection;
 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;
@@ -19,7 +18,6 @@ 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.

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

@@ -3,7 +3,6 @@ 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;
@@ -98,7 +97,7 @@ public class TestETLSupplier {
 	}
 	
 	@Test
-	public void testPatientExtension() throws IOException{
+	public void testPatientExtension() throws IOException, java.text.ParseException{
 		Observation fact = os.get();
 		Assert.assertNotNull(fact);
 		Patient p = fact.getExtension(Patient.class);
@@ -119,7 +118,7 @@ public class TestETLSupplier {
 		// nothing to do anymore
 	}
 	@Test
-	public void testVisitExtension() throws IOException{
+	public void testVisitExtension() throws IOException, java.text.ParseException{
 		Observation fact = os.get();
 		Assert.assertNotNull(fact);
 

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

 package de.sekmi.histream.scripting;
 
 import java.math.BigDecimal;
+import java.text.ParseException;
 
 import de.sekmi.histream.DateTimeAccuracy;
 import de.sekmi.histream.Observation;
-import de.sekmi.histream.Value;
 import de.sekmi.histream.impl.NumericValue;
 import de.sekmi.histream.impl.StringValue;
 
@@ -20,11 +20,11 @@ public class Fact {
 		return observation.getConceptId();
 	}
 	
-	public Fact start(String incompleteDateTime){
+	public Fact start(String incompleteDateTime) throws ParseException{
 		observation.setStartTime(DateTimeAccuracy.parsePartialIso8601(incompleteDateTime));
 		return this;
 	}
-	public Fact end(String incompleteDateTime){
+	public Fact end(String incompleteDateTime) throws ParseException{
 		observation.setEndTime(DateTimeAccuracy.parsePartialIso8601(incompleteDateTime));
 		return this;
 	}

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

 package de.sekmi.histream.scripting;
 
+import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -26,13 +27,13 @@ public class TestFacts {
 	DateTimeAccuracy defaultStart;
 	
 	@Before
-	public void setup() throws ScriptException{
+	public void setup() throws ScriptException, ParseException{
 		sem = new ScriptEngineManager();
 		engine = sem.getEngineByName("nashorn");
 		// enable strict mode
 		engine.eval("'use strict';");
 		factory = new ObservationFactoryImpl();
-	
+		
 		defaultStart =  DateTimeAccuracy.parsePartialIso8601("2016");
 		Observation[] facts = new Observation[]{
 				factory.createObservation("P1", "C1", DateTimeAccuracy.parsePartialIso8601("2011")),

pom.xml

@@ -52,14 +52,13 @@
 		</license>
 	</licenses>
 	<modules>
-		<!--
 		<module>histream-i2b2</module>
 		<module>histream-core</module>
 		<module>histream-hl7</module>
 		<module>histream-skos</module>
 		<module>histream-import</module>
 		<module>histream-export</module>
-		<module>histream-js</module>-->
+		<module>histream-js</module>
 		<module>histream-maven-plugin</module>
 		<!--
 		<module>i2b2-integration-tests</module>