de.sekmi.histream.i2b2

Class PostgresVisitStore

java.lang.Object

de.sekmi.histream.i2b2.PostgresExtension<I2b2Visit>

de.sekmi.histream.i2b2.PostgresVisitStore

All Implemented Interfaces:

Extension<I2b2Visit>, Closeable, AutoCloseable

public class PostgresVisitStore
extends PostgresExtension<I2b2Visit>
implements Closeable

Visit cache which synchronizes with an i2b2 visit_dimension table. Required non-null columns are encounter_num, patient_num, update_date.

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

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

The variable argument list for createInstance(Object...) requires the following arguments: StringvisitId, I2b2Patientpatient, ExternalSourceTypesource.

Author:

marap1

Constructor Summary

Constructors

Constructor and Description
PostgresVisitStore()

Method Summary

Modifier and Type	Method and Description
void	close()
I2b2Visit	createInstance(Object... args)
I2b2Visit	createInstance(Observation fact)
void	deleteWhereSourceId(String sourceId)
I2b2Visit	findVisit(String id) Find a visit.
void	flush() Write updates to disk.
Iterable<Class<? super I2b2Visit>>	getInstanceTypes()
void	loadMaxInstanceNums()
I2b2Visit	lookupEncounterNum(Integer encounter_num)
void	open(Connection connection, String projectId)
protected void	prepareStatements()
int	size()

Methods inherited from class de.sekmi.histream.i2b2.PostgresExtension

inaccurateSqlTimestamp

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PostgresVisitStore

public PostgresVisitStore()

Method Detail

open

public void open(Connection connection,
                 String projectId)
          throws SQLException

Throws:

SQLException

prepareStatements

protected void prepareStatements()
                          throws SQLException

Specified by:

prepareStatements in class PostgresExtension<I2b2Visit>

Throws:

SQLException

size

public int size()

lookupEncounterNum

public I2b2Visit lookupEncounterNum(Integer encounter_num)

loadMaxInstanceNums

public void loadMaxInstanceNums()
                         throws SQLException

Throws:

SQLException

createInstance

public I2b2Visit createInstance(Observation fact)

Specified by:

createInstance in interface Extension<I2b2Visit>

getInstanceTypes

public Iterable<Class<? super I2b2Visit>> getInstanceTypes()

Specified by:

getInstanceTypes in interface Extension<I2b2Visit>

findVisit

public I2b2Visit findVisit(String id)

Find a visit. Does not create the visit if it doesn't exist.

Parameters:

id - visit id/alias

Returns:

visit or null if not found.

deleteWhereSourceId

public void deleteWhereSourceId(String sourceId)
                         throws SQLException

Specified by:

deleteWhereSourceId in class PostgresExtension<I2b2Visit>

Throws:

SQLException

createInstance

public I2b2Visit createInstance(Object... args)
                         throws UnsupportedOperationException

Specified by:

createInstance in interface Extension<I2b2Visit>

Throws:

UnsupportedOperationException

flush

public void flush()

Description copied from class: PostgresExtension

Write updates to disk.

Specified by:

flush in class PostgresExtension<I2b2Visit>

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Throws:

IOException