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(Connection dbMeta, Connection dbData, Map<String,String> props)
Import(Map<String,String> props) Connect to the i2b2 database.

Method Summary

Modifier and Type	Method and Description
void	close()
int	getDeleteAccessCount()
int	getDeleteConceptCount()
int	getDeleteMetaCount()
int	getInsertAccessCount()
int	getInsertConceptCount()
int	getInsertMetaCount()
void	processOntology()
String	readableConceptPath(String path) Build a readable representation of a concept path.
void	setOntology(Ontology ontology)
void	setWarningHandler(Consumer<String> warningHandler)

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

Import

public Import(Connection dbMeta,
              Connection dbData,
              Map<String,String> props)
       throws SQLException

Throws:

SQLException

Method Detail

getInsertMetaCount

public int getInsertMetaCount()

getDeleteMetaCount

public int getDeleteMetaCount()

getInsertConceptCount

public int getInsertConceptCount()

getDeleteConceptCount

public int getDeleteConceptCount()

getInsertAccessCount

public int getInsertAccessCount()

getDeleteAccessCount

public int getDeleteAccessCount()

setWarningHandler

public void setWarningHandler(Consumer<String> warningHandler)

processOntology

public void processOntology()
                     throws SQLException,
                            OntologyException

Throws:

SQLException

OntologyException

readableConceptPath

public String readableConceptPath(String path)

Build a readable representation of a concept path. E.g. remove base path and namespace prefixes from path names

Parameters:

path - ontology path

Returns:

readable path

setOntology

public void setOntology(Ontology ontology)

close

public void close()

Specified by:

close in interface AutoCloseable