de.sekmi.histream.i2b2.ont

Class Import

java.lang.Object

de.sekmi.histream.i2b2.ont.Import

All Implemented Interfaces:

AutoCloseable

public class Import
extends Object
implements AutoCloseable

Import ontology data into i2b2.

Use the methods in the following order: constructor Import(Map), setOntology(Ontology), processOntology(), close()

Author:

Raphael

Constructor Summary

Constructors

Constructor and Description
Import(Map<String,String> props) Connect to the i2b2 database.

Method Summary

Modifier and Type	Method and Description
void	close()
static void	main(String[] args)
void	processOntology()
void	setOntology(Ontology ontology)

Methods inherited from class java.lang.Object

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

Constructor Detail

Import

public Import(Map<String,String> props)
       throws ClassNotFoundException,
              SQLException

Connect to the i2b2 database. The current implementation supports only Postgres databases for i2b2 versions >= 1.7.05(?)

Two connections are established: One for access to the metadata schema, the second for access to concept_dimension in the data schema. Connection arguments start with meta.jdbc. or data.jdbc..

Parameters:

props - connection parameters. Use meta.sourcesystem_cd for the source system. jdbc.host, jdbc.port, jdbc.database are used to construct the connect string. Any other parameters starting with jdbc. are also passed to DriverManager.getConnection(String, Properties).

More parameters: ont.language and ont.scheme.

Throws:

ClassNotFoundException - if database driver not found

SQLException - for SQL errors

Method Detail

processOntology

public void processOntology()
                     throws SQLException,
                            OntologyException

Throws:

SQLException

OntologyException

setOntology

public void setOntology(Ontology ontology)

close

public void close()

Specified by:

close in interface AutoCloseable

main

public static void main(String[] args)
                 throws FileNotFoundException,
                        IOException

Throws:

FileNotFoundException

IOException