compbio.engine

Class Configurator

java.lang.Object

compbio.engine.Configurator

public class Configurator
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CLUSTER_WORK_DIRECTORY
static boolean	IS_CLUSTER_ENGINE_ENABLED
static boolean	IS_LOCAL_ENGINE_ENABLED
static java.lang.String	LOCAL_WORK_DIRECTORY
private static org.apache.log4j.Logger	log
private static compbio.util.PropertyHelper	ph

Constructor Summary

Constructors

Constructor and Description
Configurator()

Method Summary

Modifier and Type	Method and Description
static <T> ConfiguredExecutable<T>	configureExecutable(Executable<T> executable)
static <T> ConfiguredExecutable<T>	configureExecutable(Executable<T> executable, Executable.ExecProvider provider)
static <T> ConfiguredExecutable<T>	configureExecutable(Executable<T> executable, java.util.List<FastaSequence> dataSet)
static AsyncExecutor	getAsyncEngine(ConfiguredExecutable<?> executable)
static AsyncExecutor	getAsyncEngine(ConfiguredExecutable<?> executable, Executable.ExecProvider provider)
static AsyncExecutor	getAsyncEngine(java.lang.String taskId)
(package private) static Executable.ExecProvider	getExecProvider(ConfiguredExecutable<?> executable, java.util.List<FastaSequence> dataSet) Depending on the values defined in the properties (engine.cluster.enable=true and engine.local.enable=true) return either Cluster job submission engine #JobRunner or local job submission engine #LocalRunner If both engines enabled than ask LoadBalancer for an engine.
static SyncExecutor	getSyncEngine(ConfiguredExecutable<?> executable)
static SyncExecutor	getSyncEngine(ConfiguredExecutable<?> executable, Executable.ExecProvider provider)
static java.lang.String	getWorkDirectory(java.lang.String taskId)
private static boolean	initBooleanValue(java.lang.String key)
private static java.lang.String	initClusterWorkDirectory()
private static java.lang.String	initLocalDirectory()
(package private) static boolean	isLocal(java.lang.String taskId)
(package private) static boolean	isTargetedForLocalExecution(ConfiguredExecutable<?> executable)
(package private) static <T> void	setupWorkDirectory(ConfExecutable<T> confExec, Executable.ExecProvider provider)

Methods inherited from class java.lang.Object

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

Field Detail

log

private static org.apache.log4j.Logger log

ph

private static final compbio.util.PropertyHelper ph

IS_LOCAL_ENGINE_ENABLED

public static final boolean IS_LOCAL_ENGINE_ENABLED

IS_CLUSTER_ENGINE_ENABLED

public static final boolean IS_CLUSTER_ENGINE_ENABLED

LOCAL_WORK_DIRECTORY

public static final java.lang.String LOCAL_WORK_DIRECTORY

CLUSTER_WORK_DIRECTORY

public static final java.lang.String CLUSTER_WORK_DIRECTORY

Constructor Detail

Configurator

public Configurator()

Method Detail

initBooleanValue

private static boolean initBooleanValue(java.lang.String key)

initClusterWorkDirectory

private static java.lang.String initClusterWorkDirectory()

initLocalDirectory

private static java.lang.String initLocalDirectory()

getExecProvider

static Executable.ExecProvider getExecProvider(ConfiguredExecutable<?> executable,
                                               java.util.List<FastaSequence> dataSet)
                                        throws JobSubmissionException

Depending on the values defined in the properties (engine.cluster.enable=true and engine.local.enable=true) return either Cluster job submission engine #JobRunner or local job submission engine #LocalRunner If both engines enabled than ask LoadBalancer for an engine. This method will fall back and return local engine if 1) No engines are defined in the properties or they have been defined incorrectly 2) Execution environment is Windows as the system cannot really run cluster submission from windows

Parameters:

executable -

Returns:

SyncExecutor backed up by either cluster or local engines

Throws:

JobSubmissionException

configureExecutable

public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable)
                                                       throws JobSubmissionException

Throws:

JobSubmissionException

configureExecutable

public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
                                                              java.util.List<FastaSequence> dataSet)
                                                       throws JobSubmissionException

Throws:

JobSubmissionException

setupWorkDirectory

static <T> void setupWorkDirectory(ConfExecutable<T> confExec,
                                   Executable.ExecProvider provider)

configureExecutable

public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
                                                              Executable.ExecProvider provider)
                                                       throws JobSubmissionException

Throws:

JobSubmissionException

getAsyncEngine

public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable,
                                           Executable.ExecProvider provider)

getSyncEngine

public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable,
                                         Executable.ExecProvider provider)
                                  throws JobSubmissionException

Throws:

JobSubmissionException

getAsyncEngine

public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable)

getAsyncEngine

public static AsyncExecutor getAsyncEngine(java.lang.String taskId)

getSyncEngine

public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable)
                                  throws JobSubmissionException

Throws:

JobSubmissionException

isTargetedForLocalExecution

static boolean isTargetedForLocalExecution(ConfiguredExecutable<?> executable)

isLocal

static boolean isLocal(java.lang.String taskId)

getWorkDirectory

public static java.lang.String getWorkDirectory(java.lang.String taskId)