Commit eb135839 authored by R.W.Majeed's avatar R.W.Majeed
Browse files

fixed updating visit for patient change

parent 638dcebf

histream-core/src/main/java/de/sekmi/histream/impl/SimpleVisitExtension.java

+1 −1
Original line number Diff line number Diff line
@@ -47,7 +47,7 @@ public class SimpleVisitExtension implements Extension<VisitImpl>{ 
		}

		VisitImpl visit = new VisitImpl();

		visit.setId((String)args[0]);

		visit.setPatientId(((Patient)args[1]).getId());

		visit.setPatient(((Patient)args[1]));

		ExternalSourceType source = (ExternalSourceType)args[2];

		visit.setSourceId(source.getSourceId());

		visit.setSourceTimestamp(source.getSourceTimestamp());

histream-core/src/main/java/de/sekmi/histream/impl/VisitImpl.java

+6 −2
Original line number Diff line number Diff line 
package de.sekmi.histream.impl;





import java.util.Objects;



/*

 * #%L

 * histream
@@ -24,6 +26,7 @@ package de.sekmi.histream.impl; 




import de.sekmi.histream.DateTimeAccuracy;

import de.sekmi.histream.ext.Patient;

import de.sekmi.histream.ext.StoredExtensionType;

import de.sekmi.histream.ext.Visit;
@@ -49,9 +52,10 @@ public class VisitImpl extends StoredExtensionType implements Visit { 


	public String getPatientId(){return patientId;}

	

	public void setPatientId(String patientId){

	public void setPatient(Patient patient){

		Objects.requireNonNull(patient);

		// patient id should not be changed normally.

		this.patientId = patientId;

		this.patientId = patient.getId();

		// TODO need to update dirty flag?

		markDirty(true);

	}

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/I2b2Visit.java

+12 −1
Original line number Diff line number Diff line
@@ -2,6 +2,7 @@ package de.sekmi.histream.i2b2; 


import java.time.temporal.ChronoUnit;



import de.sekmi.histream.ext.Patient;

import de.sekmi.histream.ext.Visit;



/*
@@ -65,6 +66,16 @@ public class I2b2Visit extends VisitImpl { 
	public int getNum(){return encounter_num;}

	public int getPatientNum(){return patient_num;}



	@Override

	public void setPatient(Patient patient) {

		super.setPatient(patient);

		if( patient instanceof I2b2Patient ) {

			// also set the patient_num 

			int patient_num = ((I2b2Patient)patient).getNum();

			this.patient_num = patient_num;

		}

	}



	@Override

	public String toString(){

		return "I2b2Visit(encounter_um="+encounter_num+")";

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

+24 −14
Original line number Diff line number Diff line
@@ -53,6 +53,7 @@ import de.sekmi.histream.ext.Visit.Status; 
 * <p>

 * Some optional columns are used: active_status_cd, start_date, end_date, inout_cd, location_cd, sourcesystem_cd

 * <p>

 * XXX after loading encounters, the String patientId not set anymore and always null. To determine the patientId, the patientStore is required for lookup of the patientNum

 * TODO use encounter_mapping table to map actual (source) patient_ide to internal patient_num for facts.

 * <p>

 * The variable argument list for {@link #createInstance(Object...)} requires the following arguments:
@@ -137,14 +138,14 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit> implements 
		db.setAutoCommit(true);

		prepareStatements();

		loadMaxEncounterNum();

		batchLoad();

		batchLoad(); /// XXX loading visits does not set the String patientId, for that, the patientStore would be needed

	}

	@Override

	protected void prepareStatements() throws SQLException {

		// TODO: use prefix from configuration to specify tablespace

		insert = db.prepareStatement("INSERT INTO visit_dimension(encounter_num, patient_num, import_date, download_date, sourcesystem_cd) VALUES(?,?,current_timestamp,?,?)");

		insertMapping = db.prepareStatement("INSERT INTO encounter_mapping(encounter_num, encounter_ide, encounter_ide_source, patient_ide, patient_ide_source, encounter_ide_status, project_id, import_date, download_date, sourcesystem_cd) VALUES(?,?,?,?,?,'A','"+projectId+"',current_timestamp,?,?)");

		update = db.prepareStatement("UPDATE visit_dimension SET active_status_cd=?, start_date=?, end_date=?, inout_cd=?, location_cd=?, update_date=current_timestamp, download_date=?, sourcesystem_cd=? WHERE encounter_num=?");

		update = db.prepareStatement("UPDATE visit_dimension SET patient_num=?, active_status_cd=?, start_date=?, end_date=?, inout_cd=?, location_cd=?, update_date=current_timestamp, download_date=?, sourcesystem_cd=? WHERE encounter_num=?");

		//select = db.prepareStatement("SELECT encounter_num, patient_num, active_status_cd, start_date, end_date, inout_cd, location_cd, update_date, sourcesystem_cd FROM visit_dimension WHERE patient_num=?");

		selectAll = db.prepareStatement("SELECT encounter_num, patient_num, active_status_cd, start_date, end_date, inout_cd, location_cd, download_date, sourcesystem_cd FROM visit_dimension", ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);

		selectAll.setFetchSize(fetchSize);
@@ -310,16 +311,17 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit> implements 
	

	private void updateStorage(I2b2Visit visit) throws SQLException {

		synchronized( update ){

			update.setString(1, visit.getActiveStatusCd());

			update.setTimestamp(2, dialect.encodeInstantPartial(visit.getStartTime()));

			update.setTimestamp(3, dialect.encodeInstantPartial(visit.getEndTime()));

			update.setString(4, visit.getInOutCd());

			update.setString(5, dialect.encodeLocationCd(visit.getLocationId()));

			update.setTimestamp(6, dialect.encodeInstant(visit.getSourceTimestamp()));

			update.setString(7, visit.getSourceId());

			update.setInt(1, visit.getPatientNum());

			update.setString(2, visit.getActiveStatusCd());

			update.setTimestamp(3, dialect.encodeInstantPartial(visit.getStartTime()));

			update.setTimestamp(4, dialect.encodeInstantPartial(visit.getEndTime()));

			update.setString(5, visit.getInOutCd());

			update.setString(6, dialect.encodeLocationCd(visit.getLocationId()));

			update.setTimestamp(7, dialect.encodeInstant(visit.getSourceTimestamp()));

			update.setString(8, visit.getSourceId());



			// where encounter_num=visit.getNum()

			update.setInt(8, visit.getNum());

			update.setInt(9, visit.getNum());

			int rows = update.executeUpdate();

			if( rows == 0 ){

				log.warning("UPDATE executed for visit_dimension.encounter_num="+visit.getNum()+", but no rows changed.");
@@ -368,6 +370,7 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit> implements 
	private I2b2Visit loadFromResultSet(ResultSet rs) throws SQLException{

		int id = rs.getInt(1);

		int patid = rs.getInt(2);

		// XXX String patientId is always null after loading from the database.



		// load vital status code, which contains information about

		// accuracy of birth and death dates.
@@ -426,10 +429,12 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit> implements 
		I2b2Visit visit = idCache.get(encounterId);

		

		if( visit == null ){

			// visit does not exist, create a new one



			maxEncounterNum ++;

			int encounter_num = maxEncounterNum;

			visit = new I2b2Visit(encounter_num, patient.getNum());

			visit.setPatientId(patient.getId());

			visit.setPatient(patient);

			

			// created from observation, use source metadata

			visit.setSourceId(source.getSourceId());
@@ -451,12 +456,17 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit> implements 
			// commonly, the item is modified after a call to this method,

			// but changes are written later via a call to update.

			// (otherwise, the instance would need to know whether to perform INSERT or UPDATE)

		}else if( rejectPatientChange ){

		}else {

			// visit already existing

			// verify that the patient number from the visit matches with the observation

			if( visit.getPatientNum() != patient.getNum() ){

				// throw exception to abort processing

				throw new AssertionError("Patient_num mismatch between observation and visit", null);

				if( rejectPatientChange ){

					throw new AssertionError("Patient_num mismatch for visit "+encounterId+": history says "+visit.getPatientNum()+" while data says "+patient.getNum(), null);

				}else {

					log.info("Updating visit #"+visit.getNum()+" for patient change from #"+visit.getPatientNum()+" to #"+patient.getNum());

					visit.setPatient(patient);

				}

			}

		}

		return visit;