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

Class CommandWorkflowParser

java.lang.Object

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

public class CommandWorkflowParser
extends Object

This class allow parse the workflow file.

Since:

1.0

Author:

Laurent Jourdren

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CommandWorkflowParser.StepOutputPort

Field Summary

Fields

Modifier and Type	Field	Description
static String	AVAILABLE_PROCESSORS_CONSTANT_NAME	Available processor constant name.
static String	BUILD_DATE_CONSTANT_NAME	Build date constant name.
static String	BUILD_NUMBER_CONSTANT_NAME	Build number constant name.
static String	DESIGN_FILE_PATH_CONSTANT_NAME	Design file path constant name.
static String	JOB_ID_CONSTANT_NAME	Job id constant name.
static String	JOB_PATH_CONSTANT_NAME	Logs path constant name.
static String	JOB_UUID_CONSTANT_NAME	Job UUID constant name.
static String	OUTPUT_PATH_CONSTANT_NAME	Output path constant name.
static String	VERSION_CONSTANT_NAME	Version constant name.
static String	WORKFLOW_FILE_PATH_CONSTANT_NAME	Parameters file path constant name.

Constructor Summary

Constructors

Constructor	Description
CommandWorkflowParser(DataFile file)	Public constructor.
CommandWorkflowParser(File file)	Public constructor.
CommandWorkflowParser(InputStream is)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	addConstant(String constantName, String constantValue)	Add a constant.
void	addConstant(String constantName, String constantValue, boolean evaluateValue)	Add a constant.
void	addConstants(ExecutorArguments arguments)	Add job arguments information to constants.
CommandWorkflowModel	parse()	Parse the workflow file.

Methods inherited from class java.lang.Object

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

Field Detail

VERSION_CONSTANT_NAME

public static final String VERSION_CONSTANT_NAME

Version constant name.

BUILD_NUMBER_CONSTANT_NAME

public static final String BUILD_NUMBER_CONSTANT_NAME

Build number constant name.

BUILD_DATE_CONSTANT_NAME

public static final String BUILD_DATE_CONSTANT_NAME

Build date constant name.

AVAILABLE_PROCESSORS_CONSTANT_NAME

public static final String AVAILABLE_PROCESSORS_CONSTANT_NAME

Available processor constant name.

DESIGN_FILE_PATH_CONSTANT_NAME

public static final String DESIGN_FILE_PATH_CONSTANT_NAME

Design file path constant name.

See Also:

Constant Field Values

WORKFLOW_FILE_PATH_CONSTANT_NAME

public static final String WORKFLOW_FILE_PATH_CONSTANT_NAME

Parameters file path constant name.

See Also:

Constant Field Values

OUTPUT_PATH_CONSTANT_NAME

public static final String OUTPUT_PATH_CONSTANT_NAME

Output path constant name.

See Also:

Constant Field Values

JOB_ID_CONSTANT_NAME

public static final String JOB_ID_CONSTANT_NAME

Job id constant name.

See Also:

Constant Field Values

JOB_UUID_CONSTANT_NAME

public static final String JOB_UUID_CONSTANT_NAME

Job UUID constant name.

See Also:

Constant Field Values

JOB_PATH_CONSTANT_NAME

public static final String JOB_PATH_CONSTANT_NAME

Logs path constant name.

See Also:

Constant Field Values

Constructor Detail

CommandWorkflowParser

public CommandWorkflowParser(File file)
                      throws FileNotFoundException

Public constructor.

Parameters:

file - the workflow file

Throws:

FileNotFoundException - if the file is not found

CommandWorkflowParser

public CommandWorkflowParser(DataFile file)
                      throws IOException

Public constructor.

Parameters:

file - the workflow file

Throws:

IOException - if an error occurs while opening the file

CommandWorkflowParser

public CommandWorkflowParser(InputStream is)

Public constructor.

Parameters:

is - Input stream

Method Detail

parse

public CommandWorkflowModel parse()
                           throws EoulsanException

Parse the workflow file.

Throws:

EoulsanException - if an error occurs while parsing file

addConstants

public void addConstants(ExecutorArguments arguments)
                  throws EoulsanException

Add job arguments information to constants.

Parameters:

arguments - job arguments

Throws:

EoulsanException - if an error occurs while evaluating the constant

addConstant

public void addConstant(String constantName,
                        String constantValue)
                 throws EoulsanException

Add a constant.

Parameters:

constantName - constant Name

constantValue - constant value

Throws:

EoulsanException - if an error occurs while evaluating the constant

addConstant

public void addConstant(String constantName,
                        String constantValue,
                        boolean evaluateValue)
                 throws EoulsanException

Add a constant.

Parameters:

constantName - constant Name

constantValue - constant value

evaluateValue - allow evaluate the value of the constant and start an external process to do this

Throws:

EoulsanException - if an error occurs while evaluating the constant