biolockj

Class Processor

java.lang.Object

biolockj.Processor

public class Processor
extends Object

ScriptModules that generate scripts will submit a main script to the OS for execution as a Processor.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Processor.Subprocess Class used to submit processes on their own Thread.

Constructor Summary

Constructors

Constructor and Description
Processor() Empty constructor to facilitate subprocess creation

Method Summary

Modifier and Type	Method and Description
static void	deregisterThread(Thread thread) De-register a thread, so it is not considered when shutting down the application.
static String	getBashVar(String bashVar) Return the value of the bash variable from the runtime shell.
protected String	runJob(String[] args, String label)
protected String	runJob(String[] args, String label, File workDir)
protected String	runJob(String[] args, String label, File workDir, String[] envP) Execute the command args and log output with label.
static void	runModuleMainScript(ScriptModule module) This method is called by script generating ScriptModules to update the script file-permissions to ensure they are executable by the program.
static Thread	runSubprocess(String[] args, String label) Instantiates a new Processor. String[] array used to control spacing between command/params. As if executing on terminal args[0] args[1]...
static void	setFilePermissions(String path, String permissions) Set file permissions by executing chmod "script.permissions" on generated bash scripts.
static void	submitJob(String[] args, String label) Instantiates a new Processor. String[] array used to control spacing between command/params. As if executing on terminal args[0] args[1]...
static String	submitQuery(String cmd, String label) Run script that expects a single result
static boolean	subProcAlive(Long id) Check if a specific process is alive
static boolean	subProcsAlive() Check if any Subprocess threads are still running.

Methods inherited from class java.lang.Object

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

Constructor Detail

Processor

Processor()

Empty constructor to facilitate subprocess creation

Method Detail

runJob

protected String runJob(String[] args,
                        String label,
                        File workDir,
                        String[] envP)
                 throws IOException,
                        InterruptedException

Execute the command args and log output with label.

Parameters:

args - Command args

label - Log label

Returns:

last line of process output

Throws:

IOException - if errors occur reading the InputStream

InterruptedException - if the thread process is interrupted

runJob

protected String runJob(String[] args,
                        String label)
                 throws IOException,
                        InterruptedException,
                        ConfigNotFoundException

Throws:

IOException

InterruptedException

ConfigNotFoundException

runJob

protected String runJob(String[] args,
                        String label,
                        File workDir)
                 throws IOException,
                        InterruptedException,
                        ConfigNotFoundException

Throws:

IOException

InterruptedException

ConfigNotFoundException

deregisterThread

public static void deregisterThread(Thread thread)

De-register a thread, so it is not considered when shutting down the application.

Parameters:

thread - Subprocess thread

getBashVar

public static String getBashVar(String bashVar)

Return the value of the bash variable from the runtime shell.

Parameters:

bashVar - Bash variable name

Returns:

Bash env variable value or null if not found (or undefined)

runSubprocess

public static Thread runSubprocess(String[] args,
                                   String label)

Instantiates a new Processor.
String[] array used to control spacing between command/params.
As if executing on terminal args[0] args[1]... args[n-1] as one command.

Parameters:

args - Terminal command created from args (adds 1 space between each array element)

label - to associate with the process

Returns:

Thread ID

setFilePermissions

public static void setFilePermissions(String path,
                                      String permissions)
                               throws Exception

Set file permissions by executing chmod "script.permissions" on generated bash scripts.

Parameters:

path - Target directory path

permissions - Set the chmod security bits (ex 764)

Throws:

Exception - if chmod command command fails

runModuleMainScript

public static void runModuleMainScript(ScriptModule module)
                                throws Exception

This method is called by script generating ScriptModules to update the script file-permissions to ensure they are executable by the program. Once file permissions are set, the main script (passed in the args param) is executed. Calls setFilePermissions(String, String) and runModuleMainScript(ScriptModule)

Parameters:

module - ScriptModule that is submitting its main script as a Processor

Throws:

Exception

submitJob

public static void submitJob(String[] args,
                             String label)
                      throws IOException,
                             InterruptedException,
                             ConfigNotFoundException

Instantiates a new Processor.
String[] array used to control spacing between command/params.
As if executing on terminal args[0] args[1]... args[n-1] as one command.

Parameters:

args - Terminal command created from args (adds 1 space between each array element)

label - - Process label

Throws:

IOException - if errors occur reading the InputStream

InterruptedException - if the thread process is interrupted

ConfigNotFoundException

submitQuery

public static String submitQuery(String cmd,
                                 String label)
                          throws IOException,
                                 InterruptedException,
                                 ConfigNotFoundException

Run script that expects a single result

Parameters:

cmd - Command

label - Process Label

Returns:

script output

Throws:

IOException - if errors occur reading the InputStream

InterruptedException - if the thread process is interrupted

ConfigNotFoundException

subProcAlive

public static boolean subProcAlive(Long id)

Check if a specific process is alive

Parameters:

id - - Registered thread ID

Returns:

Boolean TRUE only if the ID is alive

subProcsAlive

public static boolean subProcsAlive()

Check if any Subprocess threads are still running.

Returns:

boolean TRUE if all complete