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

static java.lang.String

CLUSTER_TASK_ID_PREFIX

Constructor Summary

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

Method Summary

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()
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()
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

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

CLUSTER_TASK_ID_PREFIX

public static final java.lang.String CLUSTER_TASK_ID_PREFIX

See Also:

Constant Field Values

Constructor Detail

ConfExecutable

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

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>

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

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>