Package fr.ens.biologie.genomique.eoulsan

Class HadoopEoulsanRuntime

java.lang.Object

fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime

fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime

public final class HadoopEoulsanRuntime
extends AbstractEoulsanRuntime

This class define the Runtime to execute low level IO operation for Eoulsan in Hadoop mode.

Since:

1.0

Author:

Laurent Jourdren

Nested Class Summary

Nested classes/interfaces inherited from class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime

AbstractEoulsanRuntime.EoulsanExecMode

Method Summary

Modifier and Type	Method	Description
org.apache.hadoop.conf.Configuration	getConfiguration()	Get Hadoop configuration.
InputStream	getInputStream(String dataSource)	Create an InputStream to load data.
AbstractEoulsanRuntime.EoulsanExecMode	getMode()	Get Eoulsan mode.
OutputStream	getOutputStream(String dataSource)	Create an OutputStream to load data.
InputStream	getRawInputStream(String dataSource)	Create a raw InputStream (without decompression of input data) to load data.
File	getTempDirectory()	Get the temporary directory.
static HadoopEoulsanRuntime	newEoulsanRuntime(org.apache.hadoop.conf.Configuration conf)	Public constructor, initialize the runtime.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime

createFileInTempDir, createTempDir, createTempDir, createTempFile, getSettings

Methods inherited from class java.lang.Object

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

Method Details

getConfiguration

public org.apache.hadoop.conf.Configuration getConfiguration()

Get Hadoop configuration.

Returns:

Hadoop Configuration object

getMode

public AbstractEoulsanRuntime.EoulsanExecMode getMode()

Description copied from class: AbstractEoulsanRuntime

Get Eoulsan mode.

Specified by:

getMode in class AbstractEoulsanRuntime

Returns:

the Eoulsan mode

getTempDirectory

public File getTempDirectory()

Description copied from class: AbstractEoulsanRuntime

Get the temporary directory.

Specified by:

getTempDirectory in class AbstractEoulsanRuntime

Returns:

the temporary directory as a File object

getInputStream

public InputStream getInputStream(String dataSource)
                           throws IOException

Description copied from class: AbstractEoulsanRuntime

Create an InputStream to load data.

Specified by:

getInputStream in class AbstractEoulsanRuntime

Parameters:

dataSource - the source of the data to load

Returns:

an InputStream corresponding to the source

Throws:

IOException - if an error occurs the InputStream

getRawInputStream

public InputStream getRawInputStream(String dataSource)
                              throws IOException

Description copied from class: AbstractEoulsanRuntime

Create a raw InputStream (without decompression of input data) to load data.

Specified by:

getRawInputStream in class AbstractEoulsanRuntime

Parameters:

dataSource - the source of the data to load

Returns:

an InputStream corresponding to the source

Throws:

IOException - if an error occurs the InputStream

getOutputStream

public OutputStream getOutputStream(String dataSource)
                             throws IOException

Description copied from class: AbstractEoulsanRuntime

Create an OutputStream to load data.

Specified by:

getOutputStream in class AbstractEoulsanRuntime

Parameters:

dataSource - the source of the data to load

Returns:

an OutputStream corresponding to the source

Throws:

IOException - if an error occurs the OutputStream

newEoulsanRuntime

public static HadoopEoulsanRuntime newEoulsanRuntime(org.apache.hadoop.conf.Configuration conf)
                                              throws IOException

Public constructor, initialize the runtime. This constructor is useful in mappers or reducers for initialize Eoulsan DataProtocols.

Parameters:

conf - Hadoop configuration of the application

Returns:

an Hadoop Eoulsan runtime

Throws:

IOException - if error occurs while creating the runtime