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(DataSource ds, Map<String,String> configuration) Create a visit store using a DataSource.
PostgresVisitStore(Map<String,String> configuration) Create a visit store using configuration settings.

Method Summary

Modifier and Type	Method and Description
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.
Class<?>[]	getInstanceTypes()
void	loadMaxInstanceNums()
protected void	prepareStatements()
int	size()

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

close, copyProperties, getConnection, getFetchSize, inaccurateSqlTimestamp, openDatabase, 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

Create a visit store using configuration settings. The project id must be specified with the key project. JDBC connection configuration is specified with the key prefixes jdbc.* and data.jdbc.*

Parameters:

configuration - key value pairs

Throws:

ClassNotFoundException - database driver not found

SQLException - SQL exceptions

PostgresVisitStore

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

Create a visit store using a DataSource. The project id must be specified with the key project.

Parameters:

ds - data source for the connection

configuration - configuration settings

Throws:

SQLException - SQL error

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()

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

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>