biolockj.util

Class ModuleUtil

java.lang.Object

biolockj.util.ModuleUtil

public class ModuleUtil
extends Object

This utility holds general methods useful for BioModule interaction and management.

Method Summary

Modifier and Type	Method and Description
static BioModule	createModuleInstance(String className) Construct a BioModule based on its className to add it to the pipeline.
static String	displayID(BioModule module) Return the module ID as a 2 digit display number (add leading zero if needed).
static String	displayName(BioModule module) Return the name of the module (or an alias if it has one).
static String	displaySignature(BioModule module)
static ClassifierModule	getClassifier(BioModule module, boolean checkAhead) Get a classifier module Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
static Integer	getMinSamplesPerWorker(BioModule module) Return the min number of samples that can be processed per worker script.
static BioModule	getModule(BioModule module, String className, boolean checkAhead) Get a module with given className unless a classifier module is found 1st. Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
static List<BioModule>	getModules(BioModule module, Boolean checkAhead) Return pipeline modules after the given module if checkAhead = TRUE Otherwise return pipeline modules before the given module. If returning the prior modules, return the pipeline modules in reverse order, so the 1st item in the list is the module immediately preceding the given module.
static BioModule	getNextModule(BioModule module) BioModules are run in the order configured. Return the module configured to run after the given module.
static Integer	getNumMaxWorkers(BioModule module) For uneven batch sizes, some workers will process 1 extra script.
static Integer	getNumWorkers(BioModule module) Get the actual number of worker scripts generated for a given module, minimum value = 1.
static BioModule	getPreviousModule(BioModule module) BioModules are run in the order configured. Return the module configured to run before the given module.
static boolean	hasExecuted(BioModule module) Return TRUE if module has executed.
static boolean	hasScripts(BioModule module) Check a BioModule for scripts to execute.
static boolean	isComplete(BioModule module) Return TRUE if module completed successfully.
static boolean	isFirstRModule(BioModule module) Test if module is the first R_Module configured in the pipeline.
static boolean	isIncomplete(BioModule module) Return TRUE if module started execution but is not complete.
static boolean	isMetadataModule(BioModule module) Method determines if the given module is a metadata-module (which does not use/modify sequence data.
static void	markComplete(BioModule module) Method creates a file named "biolockjComplete" in module root directory to document module has completed successfully.
static void	markStarted(BioModule module) Method creates a file named "biolockjStarted" in module root directory to document module has completed successfully.
static boolean	moduleExists(String className) Check if a module was in the pipeline at least once.
static File	requireSubDir(BioModule module, String subDirName) Get BioModule subdirectory File object with given name.
static boolean	subDirExists(BioModule module, String subDirName) Return TRUE if BioModule sub-directory exists

Methods inherited from class java.lang.Object

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

Method Detail

displayID

public static String displayID(BioModule module)

Return the module ID as a 2 digit display number (add leading zero if needed).

Parameters:

module - BioModule

Returns:

ID display value

displayName

public static String displayName(BioModule module)

Return the name of the module (or an alias if it has one).

Parameters:

module - BioModule

Returns:

ID display value

displaySignature

public static String displaySignature(BioModule module)

getClassifier

public static ClassifierModule getClassifier(BioModule module,
                                             boolean checkAhead)

Get a classifier module
Use checkAhead parameter to determine if we look forward or backwards starting from the given module.

Parameters:

module - Calling BioModule

checkAhead - Boolean TRUE to check for NEXT, set FALSE to check BEHIND

Returns:

BioModule

getMinSamplesPerWorker

public static Integer getMinSamplesPerWorker(BioModule module)
                                      throws ConfigNotFoundException,
                                             ConfigFormatException,
                                             Exception

Return the min number of samples that can be processed per worker script.

Parameters:

module - BioModule

Returns:

Min # samples/worker

Throws:

ConfigFormatException

ConfigNotFoundException

Exception

getModule

public static BioModule getModule(BioModule module,
                                  String className,
                                  boolean checkAhead)
                           throws Exception

Get a module with given className unless a classifier module is found 1st.
Use checkAhead parameter to determine if we look forward or backwards starting from the given module.

Parameters:

module - Calling BioModule

className - Target BioModule class name

checkAhead - Boolean TRUE to check for NEXT, set FALSE to check BEHIND

Returns:

BioModule

Throws:

Exception - if errors occur

createModuleInstance

public static BioModule createModuleInstance(String className)
                                      throws Exception

Construct a BioModule based on its className to add it to the pipeline.

Parameters:

className - BioModule class name

Returns:

BioModule module

Throws:

Exception - if errors occur

getModules

public static List<BioModule> getModules(BioModule module,
                                         Boolean checkAhead)

Return pipeline modules after the given module if checkAhead = TRUE
Otherwise return pipeline modules before the given module.
If returning the prior modules, return the pipeline modules in reverse order, so the 1st item in the list is the module immediately preceding the given module.

Parameters:

module - Reference BioModule

checkAhead - Set TRUE to return modules after the given reference module

Returns:

List of BioModules before/after the current module, as determined by checkAhead parameter

getNextModule

public static BioModule getNextModule(BioModule module)

BioModules are run in the order configured.
Return the module configured to run after the given module.

Parameters:

module - BioModule

Returns:

Next BioModule

getNumMaxWorkers

public static Integer getNumMaxWorkers(BioModule module)
                                throws Exception

For uneven batch sizes, some workers will process 1 extra script. Return the number of workers that do so.

Parameters:

module - BioModule

Returns:

Number of worker scripts that process 1 extra sequence.

Throws:

Exception

getNumWorkers

public static Integer getNumWorkers(BioModule module)
                             throws ConfigNotFoundException,
                                    ConfigFormatException

Get the actual number of worker scripts generated for a given module, minimum value = 1.

Parameters:

module - BioModule

Returns:

Number of worker scripts generated for a given module.

Throws:

ConfigFormatException

ConfigNotFoundException

Exception

getPreviousModule

public static BioModule getPreviousModule(BioModule module)

BioModules are run in the order configured.
Return the module configured to run before the given module.

Parameters:

module - BioModule

Returns:

Previous BioModule

hasExecuted

public static boolean hasExecuted(BioModule module)

Return TRUE if module has executed.

Parameters:

module - BioModule

Returns:

TRUE if module has executed

hasScripts

public static boolean hasScripts(BioModule module)

Check a BioModule for scripts to execute.

Parameters:

module - BioModule

Returns:

TRUE if the module has scripts to run

isComplete

public static boolean isComplete(BioModule module)

Return TRUE if module completed successfully.

Parameters:

module - BioModule

Returns:

TRUE if module has completed successfully.

isFirstRModule

public static boolean isFirstRModule(BioModule module)

Test if module is the first R_Module configured in the pipeline.

Parameters:

module - BioModule to test

Returns:

TRUE if module is 1st R_Module in this branch

isIncomplete

public static boolean isIncomplete(BioModule module)

Return TRUE if module started execution but is not complete.

Parameters:

module - BioModule

Returns:

TRUE if module started execution but is not complete

isMetadataModule

public static boolean isMetadataModule(BioModule module)

Method determines if the given module is a metadata-module (which does not use/modify sequence data.

Parameters:

module - BioModule in question

Returns:

TRUE if module produced exactly 1 file (metadata file)

markComplete

public static void markComplete(BioModule module)
                         throws BioLockJStatusException,
                                IOException

Method creates a file named "biolockjComplete" in module root directory to document module has completed successfully. Also clean up by removing file "biolockjStarted".

Parameters:

module - BioModule

Throws:

IOException

BioLockJStatusException

Exception - if unable to create "biolockjComplete" file

markStarted

public static void markStarted(BioModule module)
                        throws BioLockJStatusException,
                               IOException

Method creates a file named "biolockjStarted" in module root directory to document module has completed successfully. Also sets the start time and caches module name to list of executed modules so we can check later if it ran during this pipeline execution (as opposed to a previous failed run).

Parameters:

module - module

Throws:

IOException

BioLockJStatusException

Exception - if unable to create "biolockjStarted" file

moduleExists

public static boolean moduleExists(String className)

Check if a module was in the pipeline at least once.

Parameters:

className - module simple name

Returns:

boolean

requireSubDir

public static File requireSubDir(BioModule module,
                                 String subDirName)

Get BioModule subdirectory File object with given name. If directory doesn't exist, create it.

Parameters:

module - BioModule

subDirName - BioModule sub-directory name

Returns:

BioModule sub-directory File object

subDirExists

public static boolean subDirExists(BioModule module,
                                   String subDirName)

Return TRUE if BioModule sub-directory exists

Parameters:

module - BioModule

subDirName - BioModule sub-directory name

Returns:

TRUE if BioModule sub-directory exists