net.sourceforge.fluxion.datapublisher.biomart.impl
Class BiomartBeanFactory

java.lang.Object
  net.sourceforge.fluxion.datapublisher.biomart.impl.BiomartBeanFactory

All Implemented Interfaces:

BeanFactory

@ServiceProvider
public class BiomartBeanFactory
extends java.lang.Object
implements BeanFactory

An implementation of BeanFactory that generates beans from a Biomart datasource.

Version:

1.0

Author:

Tony Burdett

Constructor Summary

BiomartBeanFactory()

Method Summary

void	acquireDatasourceConnection(java.util.Map<java.lang.String,java.lang.String> connectionDetails) Acquire a connection to the underlying datasource.
boolean	dbms(java.lang.String dbms) Determines whether a BeanFactory implementation can generate beans for the given dbms.
void	donotUseTableFiltering() Use this if a single factory is used to generate multiple sets of beans, and you want to stop tables from being filtered.
void	generateBeans(java.io.File sourceDirectory, java.lang.String packageName, java.util.Set<java.lang.Class> metaBeans, java.lang.String... schemas) Generate a set of beans to model the dbms the database this factory represents.
java.util.Map<java.lang.String,java.lang.String>	getDatasourceConnectionParameters() Returns the map of connection parameters supplied for this BeanFactory.
java.lang.String	getPackageName() Returns the package name known for this BeanFactory
void	terminateDatasourceConnection() Close the connection to the underlying datasource.
void	useTableFiltering(java.io.File filterTables) Enables filtering of tables by parsing a plain text file.

Methods inherited from class java.lang.Object

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

Constructor Detail

BiomartBeanFactory

public BiomartBeanFactory()

Method Detail

dbms

public boolean dbms(java.lang.String dbms)

Description copied from interface: BeanFactory

Determines whether a BeanFactory implementation can generate beans for the given dbms. Returns true if this is a valid dbms name for this service provider, false otherwise.

Specified by:

dbms in interface BeanFactory

Parameters:

dbms - the name of the dbms for a service provider, e.g. "mysql"

Returns:

true if this service provider can generate beans for the given dbms

useTableFiltering

public void useTableFiltering(java.io.File filterTables)
                       throws java.io.IOException

Description copied from interface: BeanFactory

Enables filtering of tables by parsing a plain text file. The passed file should contain one table name per line. This file will be read in and used to restrict the list of generated OWL classes

Specified by:

useTableFiltering in interface BeanFactory

Parameters:

filterTables - the file to read that restricts the created owl classes

Throws:

java.io.IOException - if there is a problem reading from the file

donotUseTableFiltering

public void donotUseTableFiltering()

Description copied from interface: BeanFactory

Use this if a single factory is used to generate multiple sets of beans, and you want to stop tables from being filtered.

Specified by:

donotUseTableFiltering in interface BeanFactory

getDatasourceConnectionParameters

public java.util.Map<java.lang.String,java.lang.String> getDatasourceConnectionParameters()

Description copied from interface: BeanFactory

Returns the map of connection parameters supplied for this BeanFactory. If this hasn't been set, the BeanFactory should return an initialised map containing the keys required for a connection to be acquired.

Specified by:

getDatasourceConnectionParameters in interface BeanFactory

Returns:

the connection parameters set so far.

acquireDatasourceConnection

public void acquireDatasourceConnection(java.util.Map<java.lang.String,java.lang.String> connectionDetails)
                                 throws BeanGenerationException

Description copied from interface: BeanFactory

Acquire a connection to the underlying datasource. This map should contain parameters for databse URL, username, and password. Use getDatasourceConnectionParameters().keySet() to get the parameters that must be set. Or do a lookup on these key values to get the default values (e.g. "anonymous" is the default username). This way, those parameters which have been set can be used, whilst null fields will be ignored if possible (for example, in the case where password="" in accessing a public MySql database).

Specified by:

acquireDatasourceConnection in interface BeanFactory

Parameters:

connectionDetails - a map containing parameters for connection to the database.

Throws:

BeanGenerationException - if the connection could not be acquired

terminateDatasourceConnection

public void terminateDatasourceConnection()
                                   throws BeanGenerationException

Description copied from interface: BeanFactory

Close the connection to the underlying datasource. Any open connection will be closed, and it is very important that implementations of this class close all connections correclty to prevent future access problems.

Specified by:

terminateDatasourceConnection in interface BeanFactory

Throws:

BeanGenerationException - if there is a problem closing the connection

generateBeans

public void generateBeans(java.io.File sourceDirectory,
                          java.lang.String packageName,
                          java.util.Set<java.lang.Class> metaBeans,
                          java.lang.String... schemas)
                   throws BeanGenerationException

Description copied from interface: BeanFactory

Generate a set of beans to model the dbms the database this factory represents. The output directory where the generated beans should go, the package name to use for all generated sources, and (optionally) the set of annotation classes representing the metadata of this database dbms should be passed.

Specified by:

generateBeans in interface BeanFactory

Parameters:

sourceDirectory - The location for the generated source files to be written to

packageName - The package name to use for generated sources

metaBeans - the set of classes representing the database metadata

schemas - an array of database schema names to use in generating the beans

Throws:

BeanGenerationException - if the beans could not be generated

getPackageName

public java.lang.String getPackageName()

Description copied from interface: BeanFactory

Returns the package name known for this BeanFactory

Specified by:

getPackageName in interface BeanFactory

Returns:

the package name