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>, Plugin, Closeable, AutoCloseable

public class PostgresVisitStore
extends PostgresExtension<I2b2Visit>

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

Field Summary

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

config, db

Constructor Summary

Constructors

Constructor and Description
PostgresVisitStore(Map<String,String> configuration)

Method Summary

Modifier and Type	Method and Description
I2b2Visit	createInstance(Object... args)
I2b2Visit	createInstance(Observation fact)
void	deleteWhereSourceId(String sourceId)
void	flush() Write updates to disk.
Class<?>[]	getInstanceTypes()
void	loadMaxInstanceNums()
protected void	prepareStatements()
int	size()

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

close, copyProperties, getConnection, getFetchSize, inaccurateSqlTimestamp, openDatabase

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.sekmi.histream.Plugin

newInstance

Constructor Detail

PostgresVisitStore

public PostgresVisitStore(Map<String,String> configuration)
                   throws ClassNotFoundException,
                          SQLException

Throws:

ClassNotFoundException

SQLException

Method Detail

prepareStatements

protected void prepareStatements()
                          throws SQLException

Specified by:

prepareStatements in class PostgresExtension<I2b2Visit>

Throws:

SQLException

size

public int size()

loadMaxInstanceNums

public void loadMaxInstanceNums()
                         throws SQLException

Throws:

SQLException

createInstance

public I2b2Visit createInstance(Observation fact)

getInstanceTypes

public Class<?>[] getInstanceTypes()

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

Throws:

UnsupportedOperationException

flush

public void flush()

Description copied from class: PostgresExtension

Write updates to disk. The method is automatically called by PostgresExtension.close().

Specified by:

flush in class PostgresExtension<I2b2Visit>