de.sekmi.histream.i2b2

Class PostgresExtension<T>

java.lang.Object

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

Type Parameters:

T - extension instance type

All Implemented Interfaces:

Extension<T>, Plugin, Closeable, AutoCloseable

Direct Known Subclasses:

PostgresPatientStore, PostgresVisitStore

public abstract class PostgresExtension<T>
extends Object
implements Extension<T>, Plugin

Extension with database connectivity. Uses configuration properties host, port, database. The configuration is then passed to DriverManager.getConnection, which also uses postgres specific properties user, password, etc.

Author:

Raphael

Field Summary

Fields

Modifier and Type	Field and Description
protected Map<String,String>	config
protected Connection	db

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	PostgresExtension(Map<String,String> configuration)

Method Summary

Modifier and Type	Method and Description
void	close()
static void	copyProperties(Map<String,String> src, String keyPrefix, Properties dest) Each key in src that starts with keyPrefix is copied (without the prefix) and its value to dest
abstract void	deleteWhereSourceId(String sourceId)
abstract void	flush() Write updates to disk.
static Connection	getConnection(Map<String,String> props, String[] prefixes)
int	getFetchSize() Get the configuration setting for fetchSize if configured.
static Timestamp	inaccurateSqlTimestamp(DateTimeAccuracy dateTime)
protected void	openDatabase(String[] propertyPrefixes)
protected abstract void	prepareStatements()

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.Extension

createInstance, createInstance, getInstanceTypes

Methods inherited from interface de.sekmi.histream.Plugin

newInstance

Field Detail

config

protected Map<String,String> config

db

protected Connection db

Constructor Detail

PostgresExtension

protected PostgresExtension(Map<String,String> configuration)

Method Detail

getConnection

public static Connection getConnection(Map<String,String> props,
                                       String[] prefixes)
                                throws SQLException,
                                       ClassNotFoundException

Throws:

SQLException

ClassNotFoundException

copyProperties

public static void copyProperties(Map<String,String> src,
                                  String keyPrefix,
                                  Properties dest)

Each key in src that starts with keyPrefix is copied (without the prefix) and its value to dest

Parameters:

src - map containing key,value pairs

keyPrefix - prefix to match src keys

dest - destination properties

openDatabase

protected void openDatabase(String[] propertyPrefixes)
                     throws ClassNotFoundException,
                            SQLException

Throws:

ClassNotFoundException

SQLException

close

public void close()
           throws IOException

Specified by:

close in interface Plugin

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Throws:

IOException

inaccurateSqlTimestamp

public static Timestamp inaccurateSqlTimestamp(DateTimeAccuracy dateTime)

getFetchSize

public int getFetchSize()

Get the configuration setting for fetchSize if configured. Otherwise the default 10000 is returned.

Returns:

configured fetch size, or 10000 otherwise.

flush

public abstract void flush()

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

deleteWhereSourceId

public abstract void deleteWhereSourceId(String sourceId)
                                  throws SQLException

Throws:

SQLException

prepareStatements

protected abstract void prepareStatements()
                                   throws SQLException

Throws:

SQLException