compbio.engine.client

Class Util

java.lang.Object

compbio.engine.client.Util

public final class Util
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
private static org.apache.log4j.Logger	log
private static compbio.util.PropertyHelper	ph

Constructor Summary

Constructors

Constructor and Description
Util()

Method Summary

Modifier and Type	Method and Description
static java.lang.String	convertToAbsolute(java.lang.String relativePath)
static java.lang.String	getCommand(Executable.ExecProvider provider, java.lang.Class<?> clazz)
static java.lang.String	getExecProperty(java.lang.String propertySpec, java.lang.Class<?> clazz)
static java.lang.String	getExecProperty(java.lang.String propertySpec, Executable<?> exec)
static java.lang.String	getFullPath(java.lang.String workDirectory, java.lang.String fileName)
static java.lang.String	getJava() Returns the absolute path to the Java executable from JAVA_HOME
static <T> LimitsManager<T>	getLimits(java.lang.Class<T> clazz) For now just assume that all parameters which came in needs setting it will be a client responsibility to prepare RunnerConfig object then
static Executable.ExecProvider	getSupportedRuntimes(java.lang.Class<?> clazz)
static boolean	isJavaLibrary(java.lang.Class<?> clazz) Returns true of executableName.jar.file property has some value in the Executable.properties file, false otherwise.
static boolean	isMarked(java.lang.String workDirectory, JobStatus marker)
static boolean	isValidJobId(java.lang.String key)
static ConfiguredExecutable<?>	loadExecutable(java.lang.String taskId)
static java.util.Map<java.lang.String,java.lang.String>	mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified, java.util.Map<java.lang.String,java.lang.String> variables)
static void	writeFile(java.lang.String workDirectory, java.lang.String fileAndEventName, java.lang.String content, boolean override)
static boolean	writeMarker(java.lang.String workDirectory, JobStatus fileType)
static void	writeStatFile(java.lang.String workDirectory, java.lang.String fileAndEventName)

Methods inherited from class java.lang.Object

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

Field Detail

ph

private static final compbio.util.PropertyHelper ph

log

private static final org.apache.log4j.Logger log

Constructor Detail

Util

public Util()

Method Detail

isValidJobId

public static boolean isValidJobId(java.lang.String key)

writeStatFile

public static void writeStatFile(java.lang.String workDirectory,
                                 java.lang.String fileAndEventName)

writeFile

public static void writeFile(java.lang.String workDirectory,
                             java.lang.String fileAndEventName,
                             java.lang.String content,
                             boolean override)

writeMarker

public static final boolean writeMarker(java.lang.String workDirectory,
                                        JobStatus fileType)

isMarked

public static boolean isMarked(java.lang.String workDirectory,
                               JobStatus marker)

mergeEnvVariables

public static java.util.Map<java.lang.String,java.lang.String> mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified,
                                                                                 java.util.Map<java.lang.String,java.lang.String> variables)

convertToAbsolute

public static java.lang.String convertToAbsolute(java.lang.String relativePath)

getExecProperty

public static java.lang.String getExecProperty(java.lang.String propertySpec,
                                               Executable<?> exec)

getExecProperty

public static java.lang.String getExecProperty(java.lang.String propertySpec,
                                               java.lang.Class<?> clazz)

getFullPath

public static java.lang.String getFullPath(java.lang.String workDirectory,
                                           java.lang.String fileName)

getCommand

public static java.lang.String getCommand(Executable.ExecProvider provider,
                                          java.lang.Class<?> clazz)

isJavaLibrary

public static boolean isJavaLibrary(java.lang.Class<?> clazz)

Returns true of executableName.jar.file property has some value in the Executable.properties file, false otherwise.

Parameters:

clazz -

Returns:

getJava

public static java.lang.String getJava()

Returns the absolute path to the Java executable from JAVA_HOME

Returns:

returns the absolute path to the Java executable from JAVA_HOME

getSupportedRuntimes

public static Executable.ExecProvider getSupportedRuntimes(java.lang.Class<?> clazz)

loadExecutable

public static ConfiguredExecutable<?> loadExecutable(java.lang.String taskId)
                                              throws ResultNotAvailableException

Throws:

ResultNotAvailableException

getLimits

public static <T> LimitsManager<T> getLimits(java.lang.Class<T> clazz)

For now just assume that all parameters which came in needs setting it will be a client responsibility to prepare RunnerConfig object then

Parameters:

rconfig -

Returns:

public static List toOptionString(RunnerConfig rconfig) { String option = ""; List options = new ArrayList(); for (Parameter par : rconfig.getParameters()) { if (par.getPossibleValues().isEmpty()) { option = par.getOptionName(); } else { option = par.getOptionName() + "=" + par.getPossibleValues().get(0); } // separate options options.add(option); } return options; }