Commit 9e987b20 authored by R.W.Majeed's avatar R.W.Majeed
Browse files

date parsing will throw checked ParseException

parent 4fa410e4

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

+7 −4
Original line number Diff line number Diff line 
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 −21
Original line number Diff line number Diff line
@@ -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 ){
@@ -413,6 +414,7 @@ public class FlatObservationSupplier extends AbstractObservationParser implement 
				// continue;

			}else{

				// parse observation

				try{

					Record fields = new Record(fieldSeparatorPattern.split(line, maxFields));

					// fields: 0 patid, 1 encounter, 2 concept, 3: type, 4: value, 5: starttime,
@@ -435,6 +437,10 @@ public class FlatObservationSupplier extends AbstractObservationParser implement 
						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

+28 −7
Original line number Diff line number Diff line
@@ -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 ){

				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

+3 −2
Original line number Diff line number Diff line
@@ -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

+11 −2
Original line number Diff line number Diff line
@@ -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") ){

				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());

		}

		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);