Class HadoopEoulsanRuntime
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
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- fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
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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
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Nested Class Summary
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Nested classes/interfaces inherited from class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
AbstractEoulsanRuntime.EoulsanExecMode
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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, decompressInputStreamIsNeeded, getSettings
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Method Detail
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getConfiguration
public org.apache.hadoop.conf.Configuration getConfiguration()
Get Hadoop configuration.- Returns:
- Hadoop Configuration object
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getMode
public AbstractEoulsanRuntime.EoulsanExecMode getMode()
Description copied from class:AbstractEoulsanRuntime
Get Eoulsan mode.- Specified by:
getMode
in classAbstractEoulsanRuntime
- Returns:
- the Eoulsan mode
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getTempDirectory
public File getTempDirectory()
Description copied from class:AbstractEoulsanRuntime
Get the temporary directory.- Specified by:
getTempDirectory
in classAbstractEoulsanRuntime
- Returns:
- the temporary directory as a File object
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getInputStream
public InputStream getInputStream(String dataSource) throws IOException
Description copied from class:AbstractEoulsanRuntime
Create an InputStream to load data.- Specified by:
getInputStream
in classAbstractEoulsanRuntime
- Parameters:
dataSource
- the source of the data to load- Returns:
- an InputStream corresponding to the source
- Throws:
IOException
- if an error occurs the InputStream
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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 classAbstractEoulsanRuntime
- Parameters:
dataSource
- the source of the data to load- Returns:
- an InputStream corresponding to the source
- Throws:
IOException
- if an error occurs the InputStream
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getOutputStream
public OutputStream getOutputStream(String dataSource) throws IOException
Description copied from class:AbstractEoulsanRuntime
Create an OutputStream to load data.- Specified by:
getOutputStream
in classAbstractEoulsanRuntime
- Parameters:
dataSource
- the source of the data to load- Returns:
- an OutputStream corresponding to the source
- Throws:
IOException
- if an error occurs the OutputStream
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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- Throws:
IOException
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