biolockj.pipelines

Class PipelineUtil

java.lang.Object

biolockj.pipelines.PipelineUtil

public class PipelineUtil
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	allFlags

Constructor Summary

Constructors

Constructor and Description
PipelineUtil()

Method Summary

Modifier and Type	Method and Description
static String	clearStatus(File dir) Remove the current status flag of a given directory
static String	clearStatus(String dirPath) Remove the current status flag of a given directory
static boolean	discardPrecheckPipeline(File pipeDir)
static File	getMasterConfig(File pipeDir) Get the MASTER_*.properties file for a given pipeline.
static File	getMostRecentPipeline(File projDir)
static String	getPipelineId(File pipeDir)
static File	getPipelineStatusFlag() Get the status flag file of the current pipeline root.
static File	getPipelineStatusFlag(File dir) Get the status flag file for a given directory (could be a module, current pipeline, or restart pipeline).
static String	getProjectName(File pipeDir) Extract the project name from the an existing pipeline.
static String	getProjectNameFromPropFile(File config) Extract the project name from the Config file.
static boolean	isModuleDir(File dir) Determine if a given directory is a module directory in a pipeline.
static boolean	isPipelineDir(File dir) Determine if a given directory is a valid pipeline.
static boolean	isPrecheckPipeline(File pipelineDir) Determine if a given pipeline was run in precheck mode, ie using the parameter.
static File	markStatus(BioModule module, String statusFlag) Set the status of a module using a status flag file.
static File	markStatus(String statusFlag) Set the status of a module or pipeline using a status flag file.
static File	markStatus(String dirPath, String statusFlag) Set the status of a module or pipeline using a status flag file.

Methods inherited from class java.lang.Object

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

Field Detail

allFlags

public static final String[] allFlags

Constructor Detail

PipelineUtil

public PipelineUtil()

Method Detail

discardPrecheckPipeline

public static boolean discardPrecheckPipeline(File pipeDir)

Parameters:

pipeDir - the pipeline directory to discard

Returns:

boolean true if the pipeline was successfully removed.

getMostRecentPipeline

public static File getMostRecentPipeline(File projDir)

getProjectNameFromPropFile

public static String getProjectNameFromPropFile(File config)

Extract the project name from the Config file.

Parameters:

configName - file name to derive the name from

Returns:

Project name

getProjectName

public static String getProjectName(File pipeDir)
                             throws InvalidPipelineException

Extract the project name from the an existing pipeline.

Parameters:

configName - file name to derive the name from

Returns:

Project name

Throws:

InvalidPipelineException

getPipelineId

public static String getPipelineId(File pipeDir)
                            throws InvalidPipelineException

Throws:

InvalidPipelineException

isModuleDir

public static boolean isModuleDir(File dir)

Determine if a given directory is a module directory in a pipeline.

Parameters:

dir -

Returns:

isPipelineDir

public static boolean isPipelineDir(File dir)

Determine if a given directory is a valid pipeline. To be a valid pipeline, the dir must exist, be a directory, and contain a master properties file.

Parameters:

dir -

Returns:

getMasterConfig

public static File getMasterConfig(File pipeDir)
                            throws InvalidPipelineException

Get the MASTER_*.properties file for a given pipeline.

Parameters:

pipeDir - a pipeline directory

Returns:

the master config file for the pipeline

Throws:

InvalidPipelineException

isPrecheckPipeline

public static boolean isPrecheckPipeline(File pipelineDir)

Determine if a given pipeline was run in precheck mode, ie using the parameter.

Parameters:

pipelineDir -

Returns:

getPipelineStatusFlag

public static File getPipelineStatusFlag(File dir)

Get the status flag file for a given directory (could be a module, current pipeline, or restart pipeline).

Parameters:

dir -

Returns:

getPipelineStatusFlag

public static File getPipelineStatusFlag()

Get the status flag file of the current pipeline root.

Returns:

clearStatus

public static String clearStatus(File dir)

Remove the current status flag of a given directory

Parameters:

dir - The pipeline or module directory to remove the flag from

clearStatus

public static String clearStatus(String dirPath)

Remove the current status flag of a given directory

Parameters:

dirPath - a String giving the absolute path to a pipeline or module

markStatus

public static File markStatus(String dirPath,
                              String statusFlag)
                       throws BioLockJStatusException,
                              IOException

Set the status of a module or pipeline using a status flag file.

Parameters:

dirPath - the module or pipeline to mark

statusFlag - the flag to mark it with

Returns:

Throws:

BioLockJStatusException

IOException

markStatus

public static File markStatus(String statusFlag)
                       throws BioLockJStatusException,
                              IOException

Set the status of a module or pipeline using a status flag file.

Parameters:

statusFlag -

Returns:

Throws:

BioLockJStatusException

IOException

markStatus

public static File markStatus(BioModule module,
                              String statusFlag)
                       throws BioLockJStatusException,
                              IOException

Set the status of a module using a status flag file.

Parameters:

module -

statusFlag -

Returns:

Throws:

BioLockJStatusException

IOException