Commit 3c465044 authored by R.W.Majeed's avatar R.W.Majeed
Browse files

fixed patient/visit extensions for i2b2 extractor.

parent 3f27fd4d

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/DataDialect.java

+6 −0
Original line number Diff line number Diff line
@@ -86,6 +86,12 @@ public class DataDialect { 
	public String encodeUnitCd(String unitCd){

		return encodeNull(unitCd, getNullUnitCd());

	}

	public String decodeUnitCd(String rowValue){

		return decodeNull(rowValue, nullUnitCd);

	}

	public String decodeValueTypeCd(String rowValue){

		return decodeNull(rowValue, nullValueTypeCd);

	}

	public String encodeProviderId(String providerId){

		return encodeNull(providerId, getDefaultProviderId());

	}

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/I2b2Extractor.java

+78 −10
Original line number Diff line number Diff line 
package de.sekmi.histream.i2b2;



import java.math.BigDecimal;

import java.sql.Connection;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.sql.Statement;

import java.sql.Timestamp;

import java.util.logging.Logger;



import de.sekmi.histream.AbnormalFlag;

import de.sekmi.histream.DateTimeAccuracy;

import de.sekmi.histream.Observation;

import de.sekmi.histream.ObservationSupplier;

import de.sekmi.histream.Value;

import de.sekmi.histream.ext.Patient;

import de.sekmi.histream.ext.Visit;

import de.sekmi.histream.impl.ExternalSourceImpl;

import de.sekmi.histream.impl.NumericValue;

import de.sekmi.histream.impl.StringValue;



/**

 * Retrieves observations from i2b2. See {@link I2b2ExtractorFactory}.
@@ -18,6 +25,7 @@ import de.sekmi.histream.impl.ExternalSourceImpl; 
 *

 */

public class I2b2Extractor implements ObservationSupplier {

	private static final Logger log = Logger.getLogger(I2b2Extractor.class.getName());



	private I2b2ExtractorFactory factory;

	private Connection dbc;
@@ -74,8 +82,8 @@ public class I2b2Extractor implements ObservationSupplier { 
	}

	

	private static class Row{

		String pid;

		String eid;

		int pid;

		int eid;

		Integer inst;

		/** concept id */

		String cid;
@@ -86,11 +94,16 @@ public class I2b2Extractor implements ObservationSupplier { 
		Timestamp end;

		Timestamp source_ts;

		String source_cd;

		String vt;

		String vc;

		BigDecimal vn;

		AbnormalFlag vf;

		String vu;

	}

	private Row loadRow() throws SQLException{

		Row row = new Row();

		row.pid = rs.getObject(1).toString(); // patient id

		row.eid = rs.getObject(2).toString(); // encounter id

		row.pid = rs.getInt(1); // patient num

		row.eid = rs.getInt(2); // encounter num

		row.inst = rs.getInt(3);

		if( rs.wasNull() ){

			row.inst = null;
@@ -101,18 +114,71 @@ public class I2b2Extractor implements ObservationSupplier { 
		row.lid = factory.dialect.decodeLocationCd(rs.getString(7)); // location id

		row.start = rs.getTimestamp(8);

		row.end = rs.getTimestamp(9);

		// value

		row.vt = factory.dialect.decodeValueTypeCd(rs.getString(10));

		row.vc = rs.getString(11);

		row.vn = rs.getBigDecimal(12);

		row.vf = factory.dialect.decodeValueFlagCd(rs.getString(13));

		row.vu = factory.dialect.decodeUnitCd(rs.getString(14));

	

		// need source

		row.source_ts = rs.getTimestamp(15);

		row.source_cd = rs.getString(16);

		return row;

	}

	private Value createValue(Row row){

		// TODO create value

		if( row.vt == null ){

			return null; // no value

		}else if( row.vt.equals("T") ){

			StringValue v = new StringValue(row.vc);

			v.setAbnormalFlag(row.vf);

			return v;

		}else if( row.vt.equals("N") ){

			NumericValue v = new NumericValue(row.vn, row.vu);

			v.setAbnormalFlag(row.vf);

			return v;

		}else{

			log.severe("Ignoring unsupported value type '"+row.vt+"' for concept "+row.cid);

			return null;

		}

	}

	private Observation createObservation(Row row){

		Observation o = factory.getObservationFactory().createObservation(row.pid, row.cid, new DateTimeAccuracy(row.start.toLocalDateTime()));

		o.setEncounterId(row.eid);

		// map/lookup patient_num -> Patient, encounter_num -> Visit

		Patient patient = null;

		String patientId = null;

		if( factory.lookupPatientNum != null ){

			patient = factory.lookupPatientNum.apply(row.pid);

			if( patient == null ){

				log.severe("Unable to find patient with patient_num="+row.pid);

			}

		}

		if( patient != null ){

			patientId = patient.getId();

		}else{

			patientId = Integer.toString(row.pid);

		}

	

		

		Observation o = factory.getObservationFactory().createObservation(patientId, row.cid, new DateTimeAccuracy(row.start.toLocalDateTime()));

		if( patient != null ){

			o.setExtension(Patient.class, patient);

		}

		// parse visit

		Visit visit = null;

		if( factory.lookupVisitNum != null ){

			visit = factory.lookupVisitNum.apply(row.eid);

			if( visit == null ){

				log.severe("Unable to find visit with encounter_num="+row.eid);

			}

		}

		if( visit != null ){

			o.setEncounterId(visit.getId());

			o.setExtension(Visit.class, visit);

		}else{

			o.setEncounterId(Integer.toString(row.eid));

		}



		

		if( row.end != null ){

			o.setEndTime(new DateTimeAccuracy(row.end.toLocalDateTime()));

		}
@@ -126,8 +192,10 @@ public class I2b2Extractor implements ObservationSupplier { 
		return o;

	}

	private boolean isModifier(Row fact, Row modifier){

		return( fact.pid.equals(modifier.pid)

				&& fact.eid.equals(modifier.eid) 

		return( fact.pid == modifier.pid

				&& fact.eid == modifier.eid

				&& fact.inst != null // not needed for i2b2, but other tables (e.g.HIStream) may allow NULL instance num)

				&& modifier.inst != null

				&& fact.inst.equals(modifier.inst)

				&& modifier.mid != null );

	}

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/I2b2ExtractorFactory.java

+13 −0
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ import java.sql.Timestamp; 
import java.time.Instant;

import java.util.ArrayList;

import java.util.List;

import java.util.function.Function;

import java.util.logging.Logger;



import javax.sql.DataSource;
@@ -17,6 +18,8 @@ import de.sekmi.histream.ObservationException; 
import de.sekmi.histream.ObservationExtractor;

import de.sekmi.histream.ObservationFactory;

import de.sekmi.histream.ObservationSupplier;

import de.sekmi.histream.ext.Patient;

import de.sekmi.histream.ext.Visit;



/**

 * Extract observations from i2b2.
@@ -25,6 +28,7 @@ import de.sekmi.histream.ObservationSupplier; 
 * and retrieval of facts.

 * </p>

 * TODO add/use interface from histream-core

 * XXX TODO allow to map patient_num -> Patient and encounter_num -> Encounter, this must be done before the extension is accessed

 * @author R.W.Majeed

 *

 */
@@ -37,6 +41,8 @@ public class I2b2ExtractorFactory implements AutoCloseable, ObservationExtractor 
	private ObservationFactory observationFactory;

	private boolean allowWildcardConceptCodes;

	

	Function<Integer,? extends Patient> lookupPatientNum;

	Function<Integer,? extends Visit> lookupVisitNum;

	/**

	 * Boolean feature whether to allow wildcard concept keys. 

	 * <p>
@@ -62,6 +68,12 @@ public class I2b2ExtractorFactory implements AutoCloseable, ObservationExtractor 
		return observationFactory;

	}

	

	public void setPatientLookup(Function<Integer, ? extends Patient> lookup){

		this.lookupPatientNum = lookup;		

	}

	public void setVisitLookup(Function<Integer, ? extends Visit> lookup){

		this.lookupVisitNum = lookup;

	}

	public void setFeature(String feature, Object value){

		if( feature.equals(ALLOW_WILDCARD_CONCEPT_CODES) ){

			if( value instanceof Boolean ){
@@ -144,6 +156,7 @@ public class I2b2ExtractorFactory implements AutoCloseable, ObservationExtractor 
						if( false == es.equals(id) ){

							wildcardCount ++;

						}

						escaped.add(es);

					}

					ids = escaped;

					// TODO add check for overlapping wildcard concepts (e.g. A* and AB*)

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/PatientNumExtension.java

0 → 100644
+27 −0
Original line number Diff line number Diff line 
package de.sekmi.histream.i2b2;



import de.sekmi.histream.Extension;

import de.sekmi.histream.Observation;



public class PatientNumExtension implements Extension<Integer>{



	@Override

	public Integer createInstance(Observation observation) {

		// TODO Auto-generated method stub

		return null;

	}



	@Override

	public Integer createInstance(Object... args) throws UnsupportedOperationException, IllegalArgumentException {

		if( args.length != 1 || args[0] == null || !(args[0] instanceof Integer) ){

			throw new IllegalArgumentException("Expecting single Integer argument");

		}

		return (Integer)args[0];

	}



	@Override

	public Class<?>[] getInstanceTypes() {

		return new Class<?>[]{Integer.class};

	}



}

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/PostgresPatientStore.java

+4 −0
Original line number Diff line number Diff line
@@ -152,6 +152,10 @@ public class PostgresPatientStore extends PostgresExtension<I2b2Patient> impleme 
		return patientCache.get(patient_num);

	}

	

	public I2b2Patient lookupPatientNum(Integer patient_num){

		return patientCache.get(patient_num);

	}

	

	private I2b2Patient getCached(String patient_id){

		return idCache.get(patient_id);

	}