biolockj.launch

Class LaunchProcess

java.lang.Object

biolockj.launch.LaunchProcess

Direct Known Subclasses:

DockerLaunchProcess, JavaLaunchProcess

public class LaunchProcess
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	AWS_ARG
static String	BIOLOCKJ_TEST_MODE
protected static String	BIOLOCKJ_TEST_MODE_VALUE
protected static String	BLJ_ARG
protected File	BLJ_DIR
protected File	BLJ_PROJ_DIR
protected String	command
protected static String	CONFIG_ARG
protected static String	DEBUG_ARG
(package private) static String	DOCKER_ARG
protected static String	DOCKER_MAPPER_ARG
protected static String	ENV_ARG
protected HashMap<String,String>	envVars
protected static String	EXT_MODS_ARG
protected static String	FG_ARG
(package private) static String	GUI_ARG
protected File	initDir
protected File	mostRecent
protected List<String>	msgs
protected HashMap<String,String>	parameters
protected static String	PASSWORD_ARG
static String	PLS_USE_INSTALL
protected static String	PRECHECK_ARG
protected static String	PROJ_ARG
protected static String	RESTART_ARG
protected static String	UNUSED_PROPS_ARG
protected static String	WAIT_ARG

Constructor Summary

Constructors

Constructor and Description
LaunchProcess(String[] args)

Method Summary

Modifier and Type	Method and Description
protected void	assignMainArg()
protected String	catchFirstResponse(Process p)
protected void	checkBasicArgCompatibility()
(package private) String	createCmd()
(package private) void	displayArgVals()
(package private) boolean	foundNewPipeline()
protected void	gatherEnvVars()
protected File	getConfigFile()
boolean	getFlag(String key)
protected String	getMainArgVal()
protected File	getMostRecentPipeline()
String	getParameter(String key)
(package private) File	getPipedir()
protected File	getRestartDir()
(package private) void	grabPipelineLocation(String s)
(package private) static boolean	inTestMode()
protected boolean	isReplacementForPrecheck()
static void	main(String[] args)
protected void	printActionOptions()
static void	printHelp() Print the help to standard err.
static void	printHelp(PrintStream s) Print the help menu.
protected void	printInfo()
(package private) void	printPipeDir() Print the path to the pipeline root to standard out.
protected void	printPipelineStatus(int maxtime) Show the status the just-launched pipeline.
static void	printVersion() Print the version to standard out.
protected boolean	restartDirHasStatusFlag()
(package private) void	runCommand()
(package private) void	scanForKeys(String s) Scan string for specific keys which warrant specific actions.
(package private) void	setPipedir(File dir)
(package private) static void	showArgs(String process, String[] args)
protected void	watchProcess(Process p)

Methods inherited from class java.lang.Object

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

Field Detail

GUI_ARG

static final String GUI_ARG

See Also:

Constant Field Values

PASSWORD_ARG

protected static final String PASSWORD_ARG

See Also:

Constant Field Values

CONFIG_ARG

protected static final String CONFIG_ARG

See Also:

Constant Field Values

RESTART_ARG

protected static final String RESTART_ARG

See Also:

Constant Field Values

AWS_ARG

protected static final String AWS_ARG

See Also:

Constant Field Values

DOCKER_ARG

static final String DOCKER_ARG

See Also:

Constant Field Values

FG_ARG

protected static final String FG_ARG

See Also:

Constant Field Values

EXT_MODS_ARG

protected static final String EXT_MODS_ARG

See Also:

Constant Field Values

BLJ_ARG

protected static final String BLJ_ARG

See Also:

Constant Field Values

PROJ_ARG

protected static final String PROJ_ARG

See Also:

Constant Field Values

ENV_ARG

protected static final String ENV_ARG

See Also:

Constant Field Values

WAIT_ARG

protected static final String WAIT_ARG

See Also:

Constant Field Values

PRECHECK_ARG

protected static final String PRECHECK_ARG

See Also:

Constant Field Values

UNUSED_PROPS_ARG

protected static final String UNUSED_PROPS_ARG

See Also:

Constant Field Values

DEBUG_ARG

protected static final String DEBUG_ARG

See Also:

Constant Field Values

DOCKER_MAPPER_ARG

protected static final String DOCKER_MAPPER_ARG

See Also:

Constant Field Values

BIOLOCKJ_TEST_MODE

public static final String BIOLOCKJ_TEST_MODE

See Also:

Constant Field Values

BIOLOCKJ_TEST_MODE_VALUE

protected static String BIOLOCKJ_TEST_MODE_VALUE

PLS_USE_INSTALL

public static final String PLS_USE_INSTALL

See Also:

Constant Field Values

BLJ_DIR

protected File BLJ_DIR

BLJ_PROJ_DIR

protected File BLJ_PROJ_DIR

initDir

protected File initDir

mostRecent

protected File mostRecent

parameters

protected HashMap<String,String> parameters

envVars

protected HashMap<String,String> envVars

command

protected String command

msgs

protected List<String> msgs

Constructor Detail

LaunchProcess

public LaunchProcess(String[] args)
              throws EndLaunch,
                     DockerVolCreationException,
                     ConfigPathException

Throws:

EndLaunch

DockerVolCreationException

ConfigPathException

Method Detail

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception

inTestMode

static boolean inTestMode()

showArgs

static void showArgs(String process,
                     String[] args)

assignMainArg

protected void assignMainArg()

checkBasicArgCompatibility

protected void checkBasicArgCompatibility()
                                   throws EndLaunch,
                                          DockerVolCreationException

Throws:

EndLaunch

DockerVolCreationException

gatherEnvVars

protected void gatherEnvVars()
                      throws EndLaunch,
                             DockerVolCreationException,
                             ConfigPathException

Throws:

EndLaunch

DockerVolCreationException

ConfigPathException

displayArgVals

void displayArgVals()

printVersion

public static void printVersion()

Print the version to standard out. This is a rare case, usually all printing is done through ProgressUtil

printHelp

public static void printHelp()

Print the help to standard err. This is a rare case, usually all printing is done through ProgressUtil

printHelp

public static void printHelp(PrintStream s)

Print the help menu. This is a rare case, usually all printing in the launch package is done through ProgressUtil.

Parameters:

s - PrintStream; System.out or System.err

getParameter

public String getParameter(String key)

getFlag

public boolean getFlag(String key)

getMainArgVal

protected String getMainArgVal()

getConfigFile

protected File getConfigFile()

getRestartDir

protected File getRestartDir()

restartDirHasStatusFlag

protected boolean restartDirHasStatusFlag()

getMostRecentPipeline

protected File getMostRecentPipeline()

isReplacementForPrecheck

protected boolean isReplacementForPrecheck()

printInfo

protected void printInfo()
                  throws InterruptedException,
                         IOException,
                         EndLaunch

Throws:

InterruptedException

IOException

EndLaunch

printActionOptions

protected void printActionOptions()

watchProcess

protected void watchProcess(Process p)
                     throws IOException,
                            InterruptedException

Throws:

IOException

InterruptedException

catchFirstResponse

protected String catchFirstResponse(Process p)
                             throws IOException

Throws:

IOException

printPipelineStatus

protected void printPipelineStatus(int maxtime)
                            throws InterruptedException,
                                   IOException,
                                   EndLaunch

Show the status the just-launched pipeline.

Parameters:

maxtime - - maximum time in seconds to wait for a status.

Throws:

InterruptedException

IOException

EndLaunch

createCmd

String createCmd()
          throws Exception

Throws:

Exception

runCommand

void runCommand()
         throws Exception

Throws:

Exception

setPipedir

void setPipedir(File dir)

getPipedir

File getPipedir()

printPipeDir

void printPipeDir()

Print the path to the pipeline root to standard out. This is a rare case, usually all printing is done through ProgressUtil. This should be done exactly once during the launch process.

foundNewPipeline

boolean foundNewPipeline()

scanForKeys

void scanForKeys(String s)

Scan string for specific keys which warrant specific actions.

Parameters:

s -

grabPipelineLocation

void grabPipelineLocation(String s)