Package fr.ens.biologie.genomique.eoulsan.core.workflow

Class TaskContextImpl

java.lang.Object

fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl

All Implemented Interfaces:

StepConfigurationContext, TaskContext, Serializable

public class TaskContextImpl
extends Object
implements TaskContext, Serializable

This class define a task context.

Since:

2.0

Author:

Laurent Jourdren

See Also:

Serialized Form

Method Summary

Modifier and Type	Method	Description
static TaskContextImpl	deserialize(DataFile file)	Deserialize the TaskContext object.
static TaskContextImpl	deserialize(File file)	Deserialize the TaskContext object.
static TaskContextImpl	deserialize(InputStream in)	Deserialize the TaskContext object.
void	deserializeOutputData(DataFile file)	Deserialize output data.
void	deserializeOutputData(File file)	Deserialize output data.
void	deserializeOutputData(InputStream in)	Deserialize output data.
String	getCommandAuthor()	Get the command author.
String	getCommandDescription()	Get command description.
String	getCommandName()	Get the command name.
long	getContextCreationTime()	Get the creation time of the context.
String	getContextName()	Get the context name.
Step	getCurrentStep()	Get the current step.
DataFile	getDataRepositoryDirectory()	Get the data repository directory.
DataFile	getDesignFile()	Get the design file path.
fr.ens.biologie.genomique.kenetre.log.GenericLogger	getGenericLogger()	Get the generic logger.
DataFile	getHadoopWorkingPathname()	Get the Hadoop working directory.
int	getId()
Data	getInputData(InputPort port)	Get raw access to input data stored in the object.
Data	getInputData(DataFormat format)	Get the input data for an input DataType and a Sample.
Data	getInputData(String portName)	Get the input data for a port name and a Sample.
DataFile	getJarPathname()	Get the application jar path.
String	getJobDescription()	Get the job description.
DataFile	getJobDirectory()	Get the job directory.
String	getJobEnvironment()	Get the job environment.
String	getJobHost()	Get the host of the job.
String	getJobId()	Get the job id.
String	getJobUUID()	Get the UUID of the job.
File	getLocalTempDirectory()	Get local temporary directory.
DataFile	getLocalWorkingPathname()	Get the local working directory.
Logger	getLogger()	Get the logger.
Data	getOutputData(DataFormat format, Data origin)	Get the output data for an input DataType and a Sample.
Data	getOutputData(DataFormat format, String dataName)	Get the output data for an input DataType and a Sample.
Data	getOutputData(DataFormat format, String dataName, int part)	Get the output data for an input DataType and a Sample.
Data	getOutputData(String portName, Data origin)	Get the output data for a port name and a Sample.
Data	getOutputData(String portName, String dataName)	Get the output data for a port name and a Sample.
Data	getOutputData(String portName, String dataName, int part)	Get the output data for a port name and a Sample.
DataFile	getOutputDirectory()	Get the output path.
AbstractEoulsanRuntime	getRuntime()	Get EoulsanRuntime.
Settings	getSettings()	Get Eoulsan settings.
DataFile	getStepOutputDirectory()	Get the step working directory.
String	getTaskFilePrefix()	Create the prefix of a related task file.
DataFile	getTaskOutputDirectory()	Get the task output directory.
Workflow	getWorkflow()	Get the workflow description
DataFile	getWorkflowFile()	Get the workflow file path.
void	serialize(DataFile file)	Serialize the TaskContext object.
void	serialize(File file)	Serialize the TaskContext object.
void	serialize(OutputStream out)	Serialize the TaskContext object.
void	serializeOutputData(DataFile file)	Serialize output data.
void	serializeOutputData(File file)	Serialize output data.
void	serializeOutputData(OutputStream out)	Serialize output data.
void	setContextName(String contextName)	Set the context name.
String	toString()

Methods inherited from class java.lang.Object

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

Method Detail

getId

public int getId()

getContextName

public String getContextName()

Description copied from interface: TaskContext

Get the context name.

Specified by:

getContextName in interface TaskContext

Returns:

a String with the context name

getLocalWorkingPathname

public DataFile getLocalWorkingPathname()

Get the local working directory.

Returns:

Returns the local working directory

getHadoopWorkingPathname

public DataFile getHadoopWorkingPathname()

Get the Hadoop working directory.

Returns:

Returns the Hadoop working directory

getJobDirectory

public DataFile getJobDirectory()

Get the job directory.

Specified by:

getJobDirectory in interface StepConfigurationContext

Returns:

Returns the job directory

getTaskOutputDirectory

public DataFile getTaskOutputDirectory()

Get the task output directory.

Returns:

Returns the task output directory

getDataRepositoryDirectory

public DataFile getDataRepositoryDirectory()

Get the data repository directory.

Returns:

Returns the data repository directory

getOutputDirectory

public DataFile getOutputDirectory()

Description copied from interface: StepConfigurationContext

Get the output path.

Specified by:

getOutputDirectory in interface StepConfigurationContext

Returns:

Returns the output Path

getStepOutputDirectory

public DataFile getStepOutputDirectory()

Description copied from interface: StepConfigurationContext

Get the step working directory.

Specified by:

getStepOutputDirectory in interface StepConfigurationContext

Returns:

Returns the step working directory

getJobId

public String getJobId()

Description copied from interface: StepConfigurationContext

Get the job id.

Specified by:

getJobId in interface StepConfigurationContext

Returns:

the job id

getJobHost

public String getJobHost()

Description copied from interface: StepConfigurationContext

Get the host of the job.

Specified by:

getJobHost in interface StepConfigurationContext

Returns:

a string with the host of the job

getContextCreationTime

public long getContextCreationTime()

Description copied from interface: TaskContext

Get the creation time of the context.

Specified by:

getContextCreationTime in interface TaskContext

Returns:

the creation time of the context in milliseconds since epoch (1.1.1970)

getDesignFile

public DataFile getDesignFile()

Description copied from interface: StepConfigurationContext

Get the design file path.

Specified by:

getDesignFile in interface StepConfigurationContext

Returns:

the design file path

getWorkflowFile

public DataFile getWorkflowFile()

Description copied from interface: StepConfigurationContext

Get the workflow file path.

Specified by:

getWorkflowFile in interface StepConfigurationContext

Returns:

the workflow file path

getJarPathname

public DataFile getJarPathname()

Get the application jar path.

Returns:

Returns the jar path

getJobUUID

public String getJobUUID()

Description copied from interface: StepConfigurationContext

Get the UUID of the job.

Specified by:

getJobUUID in interface StepConfigurationContext

Returns:

the job UUID

getJobDescription

public String getJobDescription()

Description copied from interface: StepConfigurationContext

Get the job description.

Specified by:

getJobDescription in interface StepConfigurationContext

Returns:

the job description

getJobEnvironment

public String getJobEnvironment()

Description copied from interface: StepConfigurationContext

Get the job environment.

Specified by:

getJobEnvironment in interface StepConfigurationContext

Returns:

the job environment

getCommandName

public String getCommandName()

Description copied from interface: StepConfigurationContext

Get the command name.

Specified by:

getCommandName in interface StepConfigurationContext

Returns:

the command name

getCommandDescription

public String getCommandDescription()

Description copied from interface: StepConfigurationContext

Get command description.

Specified by:

getCommandDescription in interface StepConfigurationContext

Returns:

the command description

getCommandAuthor

public String getCommandAuthor()

Description copied from interface: StepConfigurationContext

Get the command author.

Specified by:

getCommandAuthor in interface StepConfigurationContext

Returns:

the command author

getWorkflow

public Workflow getWorkflow()

Description copied from interface: TaskContext

Get the workflow description

Specified by:

getWorkflow in interface TaskContext

Returns:

the workflow description

getCurrentStep

public Step getCurrentStep()

Description copied from interface: StepConfigurationContext

Get the current step.

Specified by:

getCurrentStep in interface StepConfigurationContext

Returns:

the current Step or null if no Step is currently running.

setContextName

public void setContextName(String contextName)

Description copied from interface: TaskContext

Set the context name.

Specified by:

setContextName in interface TaskContext

Parameters:

contextName - the name of the context

getRuntime

public AbstractEoulsanRuntime getRuntime()

Description copied from interface: StepConfigurationContext

Get EoulsanRuntime.

Specified by:

getRuntime in interface StepConfigurationContext

Returns:

the EoulsanRuntime

getSettings

public Settings getSettings()

Description copied from interface: StepConfigurationContext

Get Eoulsan settings.

Specified by:

getSettings in interface StepConfigurationContext

Returns:

the Settings

getLogger

public Logger getLogger()

Description copied from interface: StepConfigurationContext

Get the logger.

Specified by:

getLogger in interface StepConfigurationContext

Returns:

the logger

getGenericLogger

public fr.ens.biologie.genomique.kenetre.log.GenericLogger getGenericLogger()

Description copied from interface: StepConfigurationContext

Get the generic logger.

Specified by:

getGenericLogger in interface StepConfigurationContext

Returns:

the generic logger

getInputData

public Data getInputData(String portName)

Description copied from interface: TaskContext

Get the input data for a port name and a Sample.

Specified by:

getInputData in interface TaskContext

Parameters:

portName - the name of the port

Returns:

a String with the pathname

getInputData

public Data getInputData(DataFormat format)

Description copied from interface: TaskContext

Get the input data for an input DataType and a Sample.

Specified by:

getInputData in interface TaskContext

Parameters:

format - the DataFormat of the source

Returns:

a String with the pathname

getOutputData

public Data getOutputData(String portName,
                          String dataName)

Description copied from interface: TaskContext

Get the output data for a port name and a Sample.

Specified by:

getOutputData in interface TaskContext

Parameters:

portName - the name of the port

dataName - the name of the data

Returns:

a String with the pathname

getOutputData

public Data getOutputData(String portName,
                          String dataName,
                          int part)

Description copied from interface: TaskContext

Get the output data for a port name and a Sample.

Specified by:

getOutputData in interface TaskContext

Parameters:

portName - the name of the port

dataName - the name of the data

part - data part

Returns:

a String with the pathname

getOutputData

public Data getOutputData(String portName,
                          Data origin)

Description copied from interface: TaskContext

Get the output data for a port name and a Sample.

Specified by:

getOutputData in interface TaskContext

Parameters:

portName - the name of the port

origin - origin of the new data

Returns:

a String with the pathname

getOutputData

public Data getOutputData(DataFormat format,
                          String dataName)

Description copied from interface: TaskContext

Get the output data for an input DataType and a Sample.

Specified by:

getOutputData in interface TaskContext

Parameters:

format - the DataFormat of the source

dataName - the name of the data

Returns:

a String with the pathname

getOutputData

public Data getOutputData(DataFormat format,
                          String dataName,
                          int part)

Description copied from interface: TaskContext

Get the output data for an input DataType and a Sample.

Specified by:

getOutputData in interface TaskContext

Parameters:

format - the DataFormat of the source

dataName - the name of the data

part - data part

Returns:

a String with the pathname

getOutputData

public Data getOutputData(DataFormat format,
                          Data origin)

Description copied from interface: TaskContext

Get the output data for an input DataType and a Sample.

Specified by:

getOutputData in interface TaskContext

Parameters:

format - the DataFormat of the source

origin - origin of the new data

Returns:

a String with the pathname

getLocalTempDirectory

public File getLocalTempDirectory()

Description copied from interface: StepConfigurationContext

Get local temporary directory.

Specified by:

getLocalTempDirectory in interface StepConfigurationContext

Returns:

the local temporary directory

getTaskFilePrefix

public String getTaskFilePrefix()

Create the prefix of a related task file.

Returns:

a string with the prefix of the task file

getInputData

public Data getInputData(InputPort port)

Get raw access to input data stored in the object.

Parameters:

port - name of the input port

Returns:

a Data object

toString

public String toString()

Overrides:

toString in class Object

serialize

public void serialize(File file)
               throws IOException

Serialize the TaskContext object.

Parameters:

file - output DataFile

Throws:

IOException - if an error occurs while creating the file

serialize

public void serialize(DataFile file)
               throws IOException

Serialize the TaskContext object.

Parameters:

file - output DataFile

Throws:

IOException - if an error occurs while creating the file

serialize

public void serialize(OutputStream out)
               throws IOException

Serialize the TaskContext object.

Parameters:

out - output stream

Throws:

IOException - if an error occurs while creating the file

deserialize

public static TaskContextImpl deserialize(File file)
                                   throws IOException

Deserialize the TaskContext object. Warning: this method update the values of the settings of the Eoulsan runtime.

Parameters:

file - input DataFile

Throws:

IOException - if an error occurs while reading the file

deserialize

public static TaskContextImpl deserialize(DataFile file)
                                   throws IOException

Deserialize the TaskContext object. Warning: this method update the values of the settings of the Eoulsan runtime.

Parameters:

file - input DataFile

Throws:

IOException - if an error occurs while reading the file

deserialize

public static TaskContextImpl deserialize(InputStream in)
                                   throws IOException

Deserialize the TaskContext object. Warning: this method update the values of the settings of the Eoulsan runtime.

Parameters:

in - input stream

Throws:

IOException - if an error occurs while reading the file

serializeOutputData

public void serializeOutputData(File file)
                         throws IOException

Serialize output data.

Parameters:

file - output file

Throws:

IOException - if an error occurs while creating the file

serializeOutputData

public void serializeOutputData(DataFile file)
                         throws IOException

Serialize output data.

Parameters:

file - output DataFile

Throws:

IOException - if an error occurs while creating the file

serializeOutputData

public void serializeOutputData(OutputStream out)
                         throws IOException

Serialize output data.

Parameters:

out - output stream

Throws:

IOException - if an error occurs while creating the file

deserializeOutputData

public void deserializeOutputData(DataFile file)
                           throws IOException

Deserialize output data.

Parameters:

file - input datafile

Throws:

IOException - if an error occurs while reading the file

deserializeOutputData

public void deserializeOutputData(File file)
                           throws IOException

Deserialize output data.

Parameters:

file - input file

Throws:

IOException - if an error occurs while reading the file

deserializeOutputData

public void deserializeOutputData(InputStream in)
                           throws IOException

Deserialize output data.

Parameters:

in - input stream

Throws:

IOException - if an error occurs while reading the file