deprecated VisitStore.

new integrated implementation of PatientVisitCache to ensure visit/patient assignment is always in sync

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

@@ -61,4 +61,20 @@ public interface Extension<T>{
 	Class<?>[] getInstanceTypes();
 	
 	Class<T> getSlotType();
+	/**
+	 * Extract subtype information from the slot type.
+	 * E.g. a visit store can provide info about the patient
+	 * @param slotInstance slot instance type
+	 * @param subtype subtype to retrieve
+	 * @return subtype instance
+	 */
+	<U> U extractSubtype(T slotInstance, Class<U> subtype);
+
+	public static <U,T> U extractSupertype(T slotInstance, Class<U> supertype){
+		if( supertype.isInstance(slotInstance) ) {
+			return supertype.cast(slotInstance);
+		}else {
+			throw new IllegalArgumentException("Unsupported supertype "+supertype);
+		}
+	}
 }

histream-core/src/main/java/de/sekmi/histream/ext/PatientVisitStore.java

+package de.sekmi.histream.ext;
+
+import java.util.List;
+
+public interface PatientVisitStore {
+	Patient findPatient(String patientId);
+	Visit findVisit(String visitId);
+	void merge(Patient patient, String additionalId, ExternalSourceType source);
+	
+	/**
+	 * Get alias ids for the given patient (e.g. resulting from a merge) 
+	 * @param patient patient instance
+	 * @return alias ids
+	 */
+	String[] getPatientAliasIds(Patient patient);
+	
+	/**
+	 * Deletes the patient identified by given id. This method does not remove any other associated
+	 * data e.g. like visits, observations.
+	 * @param id patient id
+	 */
+	void purgePatient(String patientId);
+	void purgeVisit(String visitId);
+
+	List<? extends Visit> allVisits(Patient patient);
+}

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

@@ -9,6 +9,7 @@ import java.util.Map;
  * @author R.W.Majeed
  *
  */
+@Deprecated
 public class CachedPatientExtension extends SimplePatientExtension {
 	private Map<String, PatientImpl> cache;
 

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

@@ -32,6 +32,7 @@ import de.sekmi.histream.ext.Patient;
  * @author R.W.Majeed
  *
  */
+@Deprecated
 public class SimplePatientExtension implements Extension<PatientImpl>{
 	private final static Class<?>[] TYPES = new Class[] {Patient.class, PatientImpl.class};
 
@@ -65,4 +66,9 @@ public class SimplePatientExtension implements Extension<PatientImpl>{
 		return PatientImpl.class;
 	}
 
+	@Override
+	public <U> U extractSubtype(PatientImpl slotInstance, Class<U> subtype) {
+		return extractSubtype(slotInstance, subtype);
+	}
+
 }

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

+package de.sekmi.histream.impl;
+
+/*
+ * #%L
+ * histream
+ * %%
+ * Copyright (C) 2013 - 2015 R.W.Majeed
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+
+import de.sekmi.histream.Observation;
+
+
+import de.sekmi.histream.Extension;
+import de.sekmi.histream.ext.ExternalSourceType;
+import de.sekmi.histream.ext.Patient;
+import de.sekmi.histream.ext.Visit;
+
+public class SimplePatientVisitExtension implements Extension<VisitPatientImpl>{
+	private final static Class<?>[] TYPES = new Class[] {Visit.class,VisitPatientImpl.class,Patient.class,PatientImpl.class};
+
+	@Override
+	public Class<?>[] getInstanceTypes() {return TYPES;}
+
+	@Override
+	public VisitPatientImpl createInstance(Object... args) {
+		if( args.length != 3 
+				|| !(args[0] instanceof String)
+				|| !(args[1] instanceof String)
+				|| !(args[2] instanceof ExternalSourceType) )
+		{
+			throw new IllegalArgumentException("Need arguments Patient id, Visit id, ExternalSourceType");
+		}
+		ExternalSourceType source = (ExternalSourceType)args[2];
+		PatientImpl patient = new PatientImpl();
+		patient.setId((String)args[0]);
+		patient.setSourceId(source.getSourceId());
+		patient.setSourceTimestamp(source.getSourceTimestamp());
+		VisitPatientImpl visit = new VisitPatientImpl((String)args[1], patient, null);
+		visit.setSourceId(source.getSourceId());
+		visit.setSourceTimestamp(source.getSourceTimestamp());
+		
+		return visit;
+	}
+
+	@Override
+	public VisitPatientImpl createInstance(Observation observation) {
+		VisitPatientImpl visit = createInstance(observation.getPatientId(), observation.getEncounterId(), observation.getSource());
+		//visit.setId();
+		//visit.setPatientId(observation.getPatientId());
+		//visit.setSourceId(observation.getSourceId());
+		//visit.setSourceTimestamp(observation.getSourceTimestamp());
+		return visit;
+	}
+
+	@Override
+	public Class<VisitPatientImpl> getSlotType() {
+		return VisitPatientImpl.class;
+	}
+
+	@Override
+	public <U> U extractSubtype(VisitPatientImpl slotInstance, Class<U> subtype) {
+		if( subtype.isAssignableFrom(PatientImpl.class) ){
+			return subtype.cast(slotInstance.getPatient());
+		}else if( subtype.isInstance(slotInstance) ) {
+			return subtype.cast(slotInstance);
+		}else {
+			throw new IllegalArgumentException("Unsupported subtype "+subtype);
+		}
+	}
+
+}

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

@@ -29,6 +29,7 @@ import de.sekmi.histream.ext.ExternalSourceType;
 import de.sekmi.histream.ext.Patient;
 import de.sekmi.histream.ext.Visit;
 
+@Deprecated
 public class SimpleVisitExtension implements Extension<VisitImpl>{
 	private final static Class<?>[] TYPES = new Class[] {Visit.class, VisitImpl.class};
 
@@ -68,5 +69,9 @@ public class SimpleVisitExtension implements Extension<VisitImpl>{
 	public Class<VisitImpl> getSlotType() {
 		return VisitImpl.class;
 	}
+	@Override
+	public <U> U extractSubtype(VisitImpl slotInstance, Class<U> subtype) {
+		return extractSubtype(slotInstance, subtype);
+	}
 
 }

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

@@ -30,6 +30,7 @@ import de.sekmi.histream.ext.Patient;
 import de.sekmi.histream.ext.StoredExtensionType;
 import de.sekmi.histream.ext.Visit;
 
+@Deprecated
 public class VisitImpl extends StoredExtensionType implements Visit {
 	private DateTimeAccuracy startTime;
 	private DateTimeAccuracy endTime;

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

+package de.sekmi.histream.impl;
+
+
+import java.util.Objects;
+
+/*
+ * #%L
+ * histream
+ * %%
+ * Copyright (C) 2013 - 2015 R.W.Majeed
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+
+
+import de.sekmi.histream.DateTimeAccuracy;
+import de.sekmi.histream.ext.StoredExtensionType;
+import de.sekmi.histream.ext.Visit;
+
+public class VisitPatientImpl extends StoredExtensionType implements Visit {
+	private PatientImpl patient;
+	private DateTimeAccuracy startTime;
+	private DateTimeAccuracy endTime;
+	private Status status;
+	private String locationId;
+	private String providerId;
+	
+	/**
+	 * Empty constructor protected, only
+	 * available to overriding classes.
+	 */
+	protected VisitPatientImpl() {
+		
+	}
+	public VisitPatientImpl(String id, PatientImpl patient, DateTimeAccuracy startTime){
+		setId(id);
+		setPatient(patient);
+		this.startTime = startTime;
+	}
+	
+	public String getPatientId(){return patient.getId();}
+	
+	public void setPatient(PatientImpl patient){
+		Objects.requireNonNull(patient);
+		// patient id should not be changed normally.
+		this.patient = patient;
+		markDirty(true);
+	}
+
+	public PatientImpl getPatient() {
+		return this.patient;
+	}
+	@Override
+	public DateTimeAccuracy getStartTime() {
+		return startTime;
+	}
+
+	@Override
+	public DateTimeAccuracy getEndTime() {
+		return endTime;
+	}
+
+	@Override
+	public Status getStatus() {
+		return this.status;
+	}
+
+	@Override
+	public void setStatus(Status status) {
+		checkAndUpdateDirty(this.status, status);
+		this.status = status;
+	}
+
+	@Override
+	public String getLocationId() {
+		return locationId;
+	}
+	
+	@Override
+	public void setLocationId(String locationId){
+		checkAndUpdateDirty(this.locationId, locationId);
+		this.locationId = locationId;
+	}
+
+	@Override
+	public void setEndTime(DateTimeAccuracy endTime) {
+		checkAndUpdateDirty(this.endTime, endTime);
+		this.endTime = endTime;
+	}
+
+	@Override
+	public void setStartTime(DateTimeAccuracy startTime) {
+		checkAndUpdateDirty(this.startTime, startTime);
+		this.startTime = startTime;
+	}
+	@Override
+	public String getProviderId() {
+		return this.providerId;
+	}
+	@Override
+	public void setProviderId(String providerId) {
+		checkAndUpdateDirty(this.providerId, providerId);
+		this.providerId = providerId;
+	}
+
+	
+
+}

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/I2b2PatientVisit.java

+package de.sekmi.histream.i2b2;
+
+import java.time.temporal.ChronoUnit;
+
+import de.sekmi.histream.ext.Visit;
+import de.sekmi.histream.impl.PatientImpl;
+
+/*
+ * #%L
+ * histream
+ * %%
+ * Copyright (C) 2013 - 2015 R.W.Majeed
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import de.sekmi.histream.impl.VisitPatientImpl;
+
+
+/**
+ * I2b2 visit. The active encounter_ide is returned by {@link #getId()}.
+ * 
+ * @author Raphael
+ *
+ */
+public class I2b2PatientVisit extends VisitPatientImpl {
+
+	/**
+	 * I2b2 internal encounter id (32bit integer)
+	 */
+	private int encounter_num;
+	private int patient_num;
+	
+	/**
+	 * String id aliases for the encounter
+	 */
+	String[] aliasIds;
+	/**
+	 * Index in aliasIds for the primary alias
+	 */
+	int primaryAliasIndex;
+	
+	int maxInstanceNum;
+	
+	public I2b2PatientVisit(int encounter_num, int patient_num) {
+		super();
+		this.encounter_num = encounter_num;
+		this.patient_num = patient_num;
+		maxInstanceNum = 1;
+		// TODO set startDate, endDate
+		
+	}
+
+	public int getNum(){return encounter_num;}
+	public int getPatientNum(){return patient_num;}
+
+	@Override
+	public void setPatient(PatientImpl patient) {
+		super.setPatient(patient);
+		if( patient instanceof I2b2Patient ) {
+			// also set the patient_num 
+			int patient_num = ((I2b2Patient)patient).getNum();
+			this.patient_num = patient_num;
+		}else {
+			throw new IllegalArgumentException("Patient expected of instanceOf I2b2Patient");
+		}
+	}
+
+	@Override
+	public String toString(){
+		return "I2b2Visit(encounter_um="+encounter_num+")";
+	}
+
+	/**
+	 * Get the i2b2 vital_status_cd for this visit.
+	 * @return vital status code, see CRC_Design doc
+	 */
+	public String getActiveStatusCd(){
+		Visit visit = this;
+		char end_char=0, start_char=0;
+		if( visit.getEndTime() != null ){
+			switch( visit.getEndTime().getAccuracy() ){
+			case DAYS:
+				end_char = 0; // same meaning
+				end_char = 'Y';
+				break;
+			case MONTHS:
+				end_char = 'M';
+				break;
+			case YEARS:
+				end_char = 'X';
+				break;
+			case HOURS:
+				end_char = 'R';
+				break;
+			case MINUTES:
+				end_char = 'T';
+				break;
+			case SECONDS:
+				end_char = 'S';
+				break;
+			default:
+			}
+		}else{
+			// null end date
+			// U: unknown, O: ongoing
+			// default to unknown
+			end_char = 'U';
+		}
+
+		// start date
+		if( visit.getStartTime() != null ){
+			switch( visit.getStartTime().getAccuracy() ){
+			case DAYS:
+				start_char = 0; // same meaning
+				start_char = 'D';
+				break;
+			case MONTHS:
+				start_char = 'B';
+				break;
+			case YEARS:
+				start_char = 'F';
+				break;
+			case HOURS:
+				start_char = 'H';
+				break;
+			case MINUTES:
+				start_char = 'I';
+				break;
+			case SECONDS:
+				start_char = 'C';
+				break;
+			default:
+			}
+		}else{
+			// null start date
+			// L: unknown, A: active
+			// default to unknown
+			start_char = 'L';
+		}
+
+		if( end_char != 0 && start_char != 0 )
+			return new String(new char[]{end_char,start_char});
+		else if( end_char != 0 )
+			return new String(new char[]{end_char});
+		else if( start_char != 0 )
+			return new String(new char[]{start_char});
+		else return null; // should not happen
+	}
+
+	/**
+	 * For decoding instructions, see the i2b2 documentation CRC_Design.pdf
+	 * The vital cd can be one or two characters.
+	 * This implementation is more failsafe by using the following 
+	 * algorithm:
+	 * <ol>
+	 *  <li>For {@code null} or {@code ""} use both timestamps accurate to day
+	 *  <li>Try to decode first character as end indicator</li>
+	 *  <li>If {@code vital_cd.length > 1} use second character as start indicator, otherwise if unable to decode the end indicator, use the first character.</li>
+	 * </ol>
+	 * @param vital_cd code to indicate accuracy of start and end date
+	 */
+	public void setActiveStatusCd(String vital_cd){
+		Visit visit = this;
+		// load accuracy
+		char endIndicator = 0;
+		char startIndicator = 0;
+		if( vital_cd == null || vital_cd.length() == 0 ){
+			// start and end date accurate to day
+			// leave indicators at 0/null
+		}else{
+			// load first indicator character
+			endIndicator = vital_cd.charAt(0);
+		}
+		
+		ChronoUnit accuracy = null;
+		
+		// end date indicator
+		switch( endIndicator ){
+		case 'U': // unknown, no date
+		case 'O': // ongoing, no date
+			// set to null
+			visit.setEndTime(null);
+			break;
+		case 0:
+		case 'Y': // known, accurate to day
+			accuracy = ChronoUnit.DAYS;
+			break;
+		case 'M': // known, accurate to month
+			accuracy = ChronoUnit.MONTHS;
+			break;
+		case 'X': // known, accurate to year
+			accuracy = ChronoUnit.YEARS;
+			break;
+		case 'R': // known, accurate to hour
+			accuracy = ChronoUnit.HOURS;
+			break;
+		case 'T': // known, accurate to minute
+			accuracy = ChronoUnit.MINUTES;
+			break;
+		case 'S': // known, accurate to second
+			accuracy = ChronoUnit.SECONDS;
+			break;
+		default:
+			// no end indicator means accurate to day
+			accuracy = ChronoUnit.DAYS;
+			// no match for end date -> check for start status in first character
+			startIndicator = endIndicator;
+		}
+		// set accuracy for end time
+		if( visit.getEndTime() != null && accuracy != null ){
+			visit.getEndTime().setAccuracy(accuracy);
+		}
+		// load start indicator
+		if( vital_cd != null && vital_cd.length() > 1 ){
+			// use second character, if available
+			startIndicator = vital_cd.charAt(1);
+		}// otherwise, the first character is used if end indicator wasn't used. See default case above
+		
+		accuracy = null;
+		// start date indicator
+		switch( startIndicator ){
+		case 'L': // unknown, no date
+		case 'A': // active, no date
+			setStartTime(null);
+			break;
+		case 0: // same as D
+		case 'D': // known, accurate to day
+			accuracy = ChronoUnit.DAYS;
+			break;
+		case 'B': // known, accurate to month
+			accuracy = ChronoUnit.MONTHS;
+			break;
+		case 'F': // known, accurate to year
+			accuracy = ChronoUnit.YEARS;
+			break;
+		case 'H': // known, accurate to hour
+			accuracy = ChronoUnit.HOURS;
+			break;
+		case 'I': // known, accurate to minute
+			accuracy = ChronoUnit.MINUTES;
+			break;
+		case 'C': // known, accurate to second
+			accuracy = ChronoUnit.SECONDS;
+			break;
+		default: // default to days if unable to parse
+			accuracy = ChronoUnit.DAYS;
+		}
+		if( visit.getStartTime() != null && accuracy != null ){
+			visit.getStartTime().setAccuracy(accuracy);
+		}
+	}
+
+	public String getInOutCd(){
+		Visit patient = this;
+		if( patient.getStatus() == null )return null;
+		else switch( patient.getStatus() ){
+		case Inpatient:
+			return "I";
+		case Outpatient:
+		case Emergency: // unsupported by i2b2, map to outpatient
+			return "O";
+		default:
+			// XXX should not happen, warning
+			return null;
+		}
+	}
+
+}

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

@@ -35,6 +35,7 @@ import de.sekmi.histream.impl.VisitImpl;
  * @author Raphael
  *
  */
+@Deprecated
 public class I2b2Visit extends VisitImpl {
 
 	/**

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

@@ -40,6 +40,7 @@ import java.util.logging.Logger;
 
 
 import de.sekmi.histream.DateTimeAccuracy;
+import de.sekmi.histream.Extension;
 import de.sekmi.histream.Observation;
 import de.sekmi.histream.ext.ExternalSourceType;
 import de.sekmi.histream.ext.Patient;
@@ -652,5 +653,9 @@ public class PostgresPatientStore extends PostgresExtension<I2b2Patient> impleme
 	public Class<I2b2Patient> getSlotType() {
 		return I2b2Patient.class;
 	}
+	@Override
+	public <U> U extractSubtype(I2b2Patient slotInstance, Class<U> subtype) {
+		return Extension.extractSupertype(slotInstance, subtype);
+	}
 	
 }

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

@@ -40,6 +40,7 @@ import java.util.logging.Logger;
 
 
 import de.sekmi.histream.DateTimeAccuracy;
+import de.sekmi.histream.Extension;
 import de.sekmi.histream.Observation;
 import de.sekmi.histream.ext.ExternalSourceType;
 import de.sekmi.histream.ext.Patient;
@@ -62,6 +63,7 @@ import de.sekmi.histream.ext.Visit.Status;
  * @author marap1
  *
  */
+@Deprecated
 public class PostgresVisitStore extends PostgresExtension<I2b2Visit> implements Closeable{
 	private static final Logger log = Logger.getLogger(PostgresVisitStore.class.getName());
 	private static final Class<?>[] INSTANCE_TYPES = new Class[] {Visit.class,I2b2Visit.class};
@@ -572,5 +574,9 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit> implements
 	public Class<I2b2Visit> getSlotType() {
 		return I2b2Visit.class;
 	}
+	@Override
+	public <U> U extractSubtype(I2b2Visit slotInstance, Class<U> subtype) {
+		return Extension.extractSupertype(slotInstance, subtype);
+	}
 
 }

histream-i2b2/src/test/java/de/sekmi/histream/i2b2/TestI2b2Visit.java

@@ -10,6 +10,7 @@ import org.junit.Test;
 
 import de.sekmi.histream.DateTimeAccuracy;
 
+@Deprecated
 public class TestI2b2Visit {
 
 	private DateTimeAccuracy createAccurateTimestamp(){

histream-i2b2/src/test/java/de/sekmi/histream/i2b2/TestPostgresVisitCache.java

+package de.sekmi.histream.i2b2;
+
+/*
+ * #%L
+ * histream
+ * %%
+ * Copyright (C) 2013 - 2015 R.W.Majeed
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+
+import java.io.IOException;
+import java.sql.SQLException;
+import java.time.Instant;
+
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import de.sekmi.histream.ext.ExternalSourceType;
+import de.sekmi.histream.impl.ExternalSourceImpl;
+public class TestPostgresVisitCache  {
+	PostgresPatientVisitCache store;
+	LocalHSQLDataSource ds;
+	
+	@Before