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.

Method Summary

Modifier and Type	Method and Description
static String	getBashVar(String bashVar) Return the value of the bash variable from the runtime shell.
void	runJob(String[] args, String label) Execute the command args and log output with label.
static void	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	submit(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 void	submit(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]...

Methods inherited from class java.lang.Object

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

Method Detail

runJob

public void runJob(String[] args,
                   String label)
            throws Exception

Execute the command args and log output with label.

Parameters:

args - Command args

label - Log label

Throws:

Exception - if errors occur in the Processor

getBashVar

public static String getBashVar(String bashVar)
                         throws Exception

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)

Throws:

Exception - if errors occur running the script

runSubprocess

public static void 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

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

submit

public static void submit(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 submit(ScriptModule)

Parameters:

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

Throws:

Exception - if errors occur during execution

submit

public static void submit(String[] args,
                          String label)
                   throws Exception

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:

Exception - if errors occur during execution