ambit2.base.external

Class CommandShell<INPUT,OUTPUT>

java.lang.Object

ambit2.base.external.CommandShell<INPUT,OUTPUT>

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<INPUT,OUTPUT>

Direct Known Subclasses:

AbstractDescriptorShell, AbstractMopacShell, ShellSDFoutput, SOMEShell

public abstract class CommandShell<INPUT,OUTPUT>
extends Object
implements net.idea.modbcum.i.processors.IProcessor<INPUT,OUTPUT>

A wrapper for an external executable (OS dependent). The executable and supporting files should be available as a resource in a jar file. When requested, the files are copied under user home directory and executed from there.
To change this behaviour, override getExecutable(String, String).
OS names expected: "Mac OS","Windows","AIX","Linux","HP-UX","Solaris"

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	enabled
protected Hashtable<String,Command>	executables
protected int	exitCode
protected String	inputFile
protected Logger	logger
static String	os_FreeBSD
static String	os_LINUX
static String	os_LINUX64
static String	os_MAC
static String	os_WINDOWS
static String	os_WINDOWS7
static String	os_WINDOWSVISTA
protected String	outputFile
protected String	prefix
protected boolean	runAsync
protected String	workFolder

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	CommandShell()

Method Summary

Modifier and Type	Method and Description
String	addExecutable(String executable, String[] morefiles)
String	addExecutable(String osname, String executable, String[] morefiles)
String	addExecutableFreeBSD(String executable, String[] morefiles)
String	addExecutableLinux(String executable, String[] morefiles)
String	addExecutableLinux64(String executable, String[] morefiles)
String	addExecutableMac(String executable, String[] morefiles)
String	addExecutableWin(String executable, String[] morefiles)
void	close()
protected boolean	exitCodeOK(int exitVal)
String	getExecutable() invokes getExecutable(String, String) with System.getProperty("os.name") as argument
String	getExecutable(String osname, String osarch)
int	getExitCode()
protected String	getHomeDir(File file)
String	getHomeFromConfig(String propertiesResource, String propertyHome)
long	getID()
String	getInputFile()
static String	getMsgemptymolecule()
String	getOutputFile()
protected String	getPath(File file)
String	getWorkFolder()
protected void	initialize()
boolean	isEnabled()
void	open()
protected abstract OUTPUT	parseOutput(String path, INPUT mol) Does nothing, override with smth meaningfull
protected OUTPUT	parseOutput(String path, INPUT mol, int exitVal)
protected List<String>	prepareInput(String path, INPUT mol) Returns empty string, override with smth meaningfull
OUTPUT	process(INPUT target)
protected void	processStdOut(InputStream is)
OUTPUT	runShell(INPUT mol)
protected OUTPUT	runShell(INPUT input, String execString)
void	setEnabled(boolean enabled)
void	setExitCode(int exitCode)
void	setInputFile(String inputFile)
void	setOutputFile(String outputFile)
void	setWorkFolder(String workFolder)
protected INPUT	transform_input(INPUT input)
protected abstract OUTPUT	transform(INPUT mol)
protected OUTPUT	transform(Process process, INPUT cmd)

Methods inherited from class java.lang.Object

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

Field Detail

prefix

protected String prefix

os_MAC

public static final String os_MAC

See Also:

Constant Field Values

os_WINDOWS

public static final String os_WINDOWS

See Also:

Constant Field Values

os_WINDOWSVISTA

public static final String os_WINDOWSVISTA

See Also:

Constant Field Values

os_WINDOWS7

public static final String os_WINDOWS7

See Also:

Constant Field Values

os_LINUX

public static final String os_LINUX

See Also:

Constant Field Values

os_LINUX64

public static final String os_LINUX64

See Also:

Constant Field Values

os_FreeBSD

public static final String os_FreeBSD

See Also:

Constant Field Values

workFolder

protected String workFolder

logger

protected Logger logger

executables

protected Hashtable<String,Command> executables

inputFile

protected String inputFile

outputFile

protected String outputFile

runAsync

protected boolean runAsync

enabled

protected boolean enabled

exitCode

protected int exitCode

Constructor Detail

CommandShell

protected CommandShell()
                throws ShellException

Throws:

ShellException

Method Detail

getWorkFolder

public String getWorkFolder()

setWorkFolder

public void setWorkFolder(String workFolder)

getMsgemptymolecule

public static String getMsgemptymolecule()

getID

public long getID()

Specified by:

getID in interface net.idea.modbcum.i.processors.IProcessor<INPUT,OUTPUT>

isEnabled

public boolean isEnabled()

Specified by:

isEnabled in interface net.idea.modbcum.i.processors.IProcessor<INPUT,OUTPUT>

setEnabled

public void setEnabled(boolean enabled)

Specified by:

setEnabled in interface net.idea.modbcum.i.processors.IProcessor<INPUT,OUTPUT>

getExitCode

public int getExitCode()

setExitCode

public void setExitCode(int exitCode)

initialize

protected void initialize()
                   throws ShellException

Throws:

ShellException

addExecutable

public String addExecutable(String executable,
                            String[] morefiles)
                     throws ShellException

Throws:

ShellException

addExecutable

public String addExecutable(String osname,
                            String executable,
                            String[] morefiles)
                     throws ShellException

Throws:

ShellException

addExecutableMac

public String addExecutableMac(String executable,
                               String[] morefiles)
                        throws ShellException

Throws:

ShellException

addExecutableWin

public String addExecutableWin(String executable,
                               String[] morefiles)
                        throws ShellException

Throws:

ShellException

addExecutableLinux

public String addExecutableLinux(String executable,
                                 String[] morefiles)
                          throws ShellException

Throws:

ShellException

addExecutableLinux64

public String addExecutableLinux64(String executable,
                                   String[] morefiles)
                            throws ShellException

Throws:

ShellException

addExecutableFreeBSD

public String addExecutableFreeBSD(String executable,
                                   String[] morefiles)
                            throws ShellException

Throws:

ShellException

getExecutable

public String getExecutable(String osname,
                            String osarch)
                     throws Exception

Throws:

Exception

getExecutable

public String getExecutable()
                     throws ShellException

invokes getExecutable(String, String) with System.getProperty("os.name") as argument

Returns:

absolute path to the executable

Throws:

ShellException

runShell

public OUTPUT runShell(INPUT mol)
                throws ShellException

Throws:

ShellException

process

public OUTPUT process(INPUT target)
               throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

process in interface net.idea.modbcum.i.processors.IProcessor<INPUT,OUTPUT>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

prepareInput

protected List<String> prepareInput(String path,
                                    INPUT mol)
                             throws ShellException

Returns empty string, override with smth meaningfull

Parameters:

mol -

Returns:

list of command line parameters (exe name excluded) to be passed to the executable

Throws:

ShellException

parseOutput

protected abstract OUTPUT parseOutput(String path,
                                      INPUT mol)
                               throws ShellException

Does nothing, override with smth meaningfull

Throws:

ShellException

parseOutput

protected OUTPUT parseOutput(String path,
                             INPUT mol,
                             int exitVal)
                      throws ShellException

Throws:

ShellException

getPath

protected String getPath(File file)

getHomeDir

protected String getHomeDir(File file)

transform_input

protected INPUT transform_input(INPUT input)
                         throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

runShell

protected OUTPUT runShell(INPUT input,
                          String execString)
                   throws ShellException

Throws:

ShellException

processStdOut

protected void processStdOut(InputStream is)
                      throws IOException

Throws:

IOException

transform

protected OUTPUT transform(Process process,
                           INPUT cmd)

exitCodeOK

protected boolean exitCodeOK(int exitVal)

getInputFile

public String getInputFile()

setInputFile

public void setInputFile(String inputFile)

getOutputFile

public String getOutputFile()

setOutputFile

public void setOutputFile(String outputFile)

transform

protected abstract OUTPUT transform(INPUT mol)

open

public void open()
          throws Exception

Specified by:

open in interface net.idea.modbcum.i.processors.IProcessor<INPUT,OUTPUT>

Throws:

Exception

close

public void close()
           throws Exception

Specified by:

close in interface net.idea.modbcum.i.processors.IProcessor<INPUT,OUTPUT>

Throws:

Exception

getHomeFromConfig

public String getHomeFromConfig(String propertiesResource,
                                String propertyHome)
                         throws ShellException

Throws:

ShellException