compbio.engine.client

Class ConfExecutable<T>

java.lang.Object

compbio.engine.client.ConfExecutable<T>

All Implemented Interfaces:

ConfiguredExecutable<T>, Executable<T>, PipedExecutable<T>

public class ConfExecutable<T>
extends java.lang.Object
implements ConfiguredExecutable<T>

Nested Class Summary

Nested classes/interfaces inherited from interface compbio.engine.client.Executable

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CLUSTER_TASK_ID_PREFIX
private Executable<T>	exec
private static org.apache.log4j.Logger	log
private static compbio.util.PropertyHelper	ph
private Executable.ExecProvider	provider
private java.lang.String	taskDirectory
private java.lang.String	workDirectory

Constructor Summary

Constructors

Constructor and Description
ConfExecutable(Executable<T> executable, java.lang.String taskDirectory)
ConfExecutable(RunConfiguration rconf)

Method Summary

Modifier and Type	Method and Description
Executable<T>	addParameters(java.util.List<java.lang.String> parameters) Adds parameter to the list of parameters for a native executable
java.lang.String	getClusterJobSettings()
java.lang.String	getCommand(Executable.ExecProvider provider)
java.util.List<java.lang.String>	getCreatedFiles()
java.util.Map<java.lang.String,java.lang.String>	getEnvironment()
java.lang.String	getError()
Executable.ExecProvider	getExecProvider()
Executable<T>	getExecutable()
(package private) java.util.List<java.lang.String>	getFullPath(java.util.List<java.lang.String> fileNames)
java.lang.String	getInput() Not all input paths are relative! Input path could be absolute!
Limit<T>	getLimit(java.lang.String presetName)
LimitsManager<T>	getLimits()
java.lang.String	getOutput()
CommandBuilder<T>	getParameters()
CommandBuilder<T>	getParameters(Executable.ExecProvider provider)
<V> V	getResults()
<V> V	getResults(java.lang.String directory)
RunConfiguration	getRunConfiguration()
(package private) static <V> java.lang.Object	getRunnerConfiguration(java.lang.Class<V> clazz, java.lang.Class<?> configurationHolder, java.lang.String propertyName)
static <V> LimitsManager<V>	getRunnerLimits(java.lang.Class<V> clazz) This method should be executed once and result of its execution reused.
static <V> RunnerConfig<V>	getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz)
static <V> PresetManager<V>	getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz)
Executable.ExecProvider	getSupportedRuntimes()
java.lang.String	getTaskId()
java.lang.String	getWorkDirectory()
ConfiguredExecutable<?>	loadRunConfiguration(java.io.InputStream input)
ConfiguredExecutable<?>	loadRunConfiguration(RunConfiguration rconf)
static ConfiguredExecutable<?>	newConfExecutable(RunConfiguration rconf)
boolean	saveRunConfiguration()
void	setExecProvider(Executable.ExecProvider provider)
void	setWorkDirectory(java.lang.String workDirectory)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

log

private static final org.apache.log4j.Logger log

ph

private static final compbio.util.PropertyHelper ph

CLUSTER_TASK_ID_PREFIX

public static final java.lang.String CLUSTER_TASK_ID_PREFIX

See Also:

Constant Field Values

workDirectory

private java.lang.String workDirectory

taskDirectory

private java.lang.String taskDirectory

provider

private Executable.ExecProvider provider

exec

private Executable<T> exec

Constructor Detail

ConfExecutable

public ConfExecutable(Executable<T> executable,
                      java.lang.String taskDirectory)

ConfExecutable

ConfExecutable(RunConfiguration rconf)

Method Detail

getExecProvider

public Executable.ExecProvider getExecProvider()

Specified by:

getExecProvider in interface ConfiguredExecutable<T>

setExecProvider

public void setExecProvider(Executable.ExecProvider provider)

getCommand

public java.lang.String getCommand(Executable.ExecProvider provider)
                            throws UnsupportedRuntimeException

Specified by:

getCommand in interface ConfiguredExecutable<T>

Throws:

UnsupportedRuntimeException

getSupportedRuntimes

public Executable.ExecProvider getSupportedRuntimes()

Specified by:

getSupportedRuntimes in interface ConfiguredExecutable<T>

getLimit

public Limit<T> getLimit(java.lang.String presetName)

Specified by:

getLimit in interface Executable<T>

getLimits

public LimitsManager<T> getLimits()

Specified by:

getLimits in interface Executable<T>

getTaskId

public java.lang.String getTaskId()

Specified by:

getTaskId in interface ConfiguredExecutable<T>

setWorkDirectory

public void setWorkDirectory(java.lang.String workDirectory)

Specified by:

setWorkDirectory in interface ConfiguredExecutable<T>

getWorkDirectory

public java.lang.String getWorkDirectory()

Specified by:

getWorkDirectory in interface ConfiguredExecutable<T>

addParameters

public Executable<T> addParameters(java.util.List<java.lang.String> parameters)

Description copied from interface: Executable

Adds parameter to the list of parameters for a native executable

Specified by:

addParameters in interface Executable<T>

Returns:

this Executable

getOutput

public java.lang.String getOutput()

Specified by:

getOutput in interface Executable<T>

getError

public java.lang.String getError()

Specified by:

getError in interface Executable<T>

getCreatedFiles

public java.util.List<java.lang.String> getCreatedFiles()

Specified by:

getCreatedFiles in interface Executable<T>

getFullPath

java.util.List<java.lang.String> getFullPath(java.util.List<java.lang.String> fileNames)

getInput

public java.lang.String getInput()

Not all input paths are relative! Input path could be absolute!

Specified by:

getInput in interface Executable<T>

See Also:

compbio.engine.client.Executable#getInputFiles()

getParameters

public CommandBuilder<T> getParameters()

Specified by:

getParameters in interface ConfiguredExecutable<T>

getParameters

public CommandBuilder<T> getParameters(Executable.ExecProvider provider)

Specified by:

getParameters in interface Executable<T>

getExecutable

public Executable<T> getExecutable()

Specified by:

getExecutable in interface ConfiguredExecutable<T>

getResults

public <V> V getResults()
                 throws ResultNotAvailableException

Specified by:

getResults in interface ConfiguredExecutable<T>

Throws:

ResultNotAvailableException

getResults

public <V> V getResults(java.lang.String directory)
                 throws ResultNotAvailableException

Specified by:

getResults in interface Executable<T>

Throws:

ResultNotAvailableException

getRunnerOptions

public static <V> RunnerConfig<V> getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz)
                                            throws java.io.IOException

Throws:

java.io.IOException

getRunnerPresets

public static <V> PresetManager<V> getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz)
                                             throws java.io.IOException

Throws:

java.io.IOException

getRunnerLimits

public static <V> LimitsManager<V> getRunnerLimits(java.lang.Class<V> clazz)
                                            throws java.io.IOException

This method should be executed once and result of its execution reused. If not used carefully it could slow down the system!

Type Parameters:

V -

Parameters:

clazz -

Returns:

LimitsManager instance

Throws:

java.io.IOException

getRunnerConfiguration

static <V> java.lang.Object getRunnerConfiguration(java.lang.Class<V> clazz,
                                                   java.lang.Class<?> configurationHolder,
                                                   java.lang.String propertyName)
                                            throws java.io.IOException

Throws:

java.io.IOException

getEnvironment

public java.util.Map<java.lang.String,java.lang.String> getEnvironment()

Specified by:

getEnvironment in interface ConfiguredExecutable<T>

loadRunConfiguration

public ConfiguredExecutable<?> loadRunConfiguration(RunConfiguration rconf)

Specified by:

loadRunConfiguration in interface Executable<T>

newConfExecutable

public static ConfiguredExecutable<?> newConfExecutable(RunConfiguration rconf)

saveRunConfiguration

public boolean saveRunConfiguration()
                             throws java.io.IOException

Specified by:

saveRunConfiguration in interface ConfiguredExecutable<T>

Throws:

java.io.IOException

getRunConfiguration

public RunConfiguration getRunConfiguration()

loadRunConfiguration

public ConfiguredExecutable<?> loadRunConfiguration(java.io.InputStream input)
                                             throws java.io.IOException

Specified by:

loadRunConfiguration in interface ConfiguredExecutable<T>

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getClusterJobSettings

public java.lang.String getClusterJobSettings()

Specified by:

getClusterJobSettings in interface Executable<T>