org.utgenome.shell
Class UTGBShellCommand

java.lang.Object
  org.utgenome.core.cui.UTGBCommandBase
      org.utgenome.shell.UTGBShellCommandBase
          org.utgenome.shell.UTGBShellCommand

All Implemented Interfaces:

Comparable<org.xerial.util.opt.Command>, org.xerial.util.opt.Command

Direct Known Subclasses:

AddAction, Clean, Compile, Create, Deploy, Eclipse, FastqRename, FastqToFasta, FastqToSAM, GWT, GWTCompile, Illumina2Fastq, Import, Keyword, Maven, Pack, QSeqToFastq, Repair, Sam2Wig, SAMToFastq, Sequence, Server, SVNAdd, Upgrade

public abstract class UTGBShellCommand
extends UTGBShellCommandBase
implements Comparable<org.xerial.util.opt.Command>

A base implementation of the UTGBShell's sub commands

Author:

leo

Field Summary

static String	APP_FOLDER
static String	EXPLODED_WEBAPP_DIR
static String	SRC_FOLDER
static String	WEBAPP_FOLDER

Fields inherited from class org.utgenome.shell.UTGBShellCommandBase

globalOption

Constructor Summary

UTGBShellCommand()

Method Summary

int	compareTo(org.xerial.util.opt.Command o)
void	createContextXML(String contextPath, String projectRoot, boolean reloadable)
void	createFileFromTemplate(Class<?> baseClass, String templateFilePath, String relativePathOfTarget, Properties prop)
static void	createFileFromTemplate(Class<?> baseClass, String templateFilePath, String projectFolder, String relativePathOfTarget, Properties prop, boolean overWrite)
abstract void	execute(String[] args)
void	execute(UTGBShell.UTGBShellOption opt, String[] args)
File	getConfigFile()
URL	getHelpMessageResource()
File	getObsolteConfigurationFile()
String	getOneLineDescription()
abstract String	getOneLinerDescription()
Object	getOptionHolder()
static String	getPath(File f)
File	getProjectResourcePath(String relativePathFromTheProjectRoot)
File	getProjectRoot()
boolean	isInProjectRoot()
UTGBConfig	loadUTGBConfig()
void	maven(String commandLine)
void	maven(String commandLine, Properties systemProperties)
abstract String	name()

Methods inherited from class org.utgenome.shell.UTGBShellCommandBase

execute

Methods inherited from class java.lang.Object

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

Field Detail

APP_FOLDER

public static final String APP_FOLDER

See Also:

Constant Field Values

SRC_FOLDER

public static final String SRC_FOLDER

See Also:

Constant Field Values

WEBAPP_FOLDER

public static final String WEBAPP_FOLDER

See Also:

Constant Field Values

EXPLODED_WEBAPP_DIR

public static final String EXPLODED_WEBAPP_DIR

See Also:

Constant Field Values

Constructor Detail

UTGBShellCommand

public UTGBShellCommand()

Method Detail

name

public abstract String name()

Specified by:

name in interface org.xerial.util.opt.Command

Specified by:

name in class UTGBCommandBase

execute

public void execute(UTGBShell.UTGBShellOption opt,
                    String[] args)
             throws Exception

Throws:

Exception

execute

public abstract void execute(String[] args)
                      throws Exception

Specified by:

execute in interface org.xerial.util.opt.Command

Specified by:

execute in class UTGBCommandBase

Throws:

Exception

getHelpMessageResource

public URL getHelpMessageResource()

Specified by:

getHelpMessageResource in interface org.xerial.util.opt.Command

Overrides:

getHelpMessageResource in class UTGBCommandBase

getOneLineDescription

public String getOneLineDescription()

Specified by:

getOneLineDescription in interface org.xerial.util.opt.Command

Specified by:

getOneLineDescription in class UTGBCommandBase

getOneLinerDescription

public abstract String getOneLinerDescription()

getOptionHolder

public Object getOptionHolder()

Specified by:

getOptionHolder in interface org.xerial.util.opt.Command

Overrides:

getOptionHolder in class UTGBCommandBase

getProjectRoot

public File getProjectRoot()

isInProjectRoot

public boolean isInProjectRoot()

getProjectResourcePath

public File getProjectResourcePath(String relativePathFromTheProjectRoot)

getConfigFile

public File getConfigFile()

getObsolteConfigurationFile

public File getObsolteConfigurationFile()

maven

public void maven(String commandLine)
           throws UTGBShellException

Throws:

UTGBShellException

maven

public void maven(String commandLine,
                  Properties systemProperties)
           throws UTGBShellException

Throws:

UTGBShellException

loadUTGBConfig

public UTGBConfig loadUTGBConfig()
                          throws UTGBShellException

Throws:

UTGBShellException

compareTo

public int compareTo(org.xerial.util.opt.Command o)

Specified by:

compareTo in interface Comparable<org.xerial.util.opt.Command>

getPath

public static String getPath(File f)

createContextXML

public void createContextXML(String contextPath,
                             String projectRoot,
                             boolean reloadable)
                      throws UTGBShellException

Throws:

UTGBShellException

createFileFromTemplate

public void createFileFromTemplate(Class<?> baseClass,
                                   String templateFilePath,
                                   String relativePathOfTarget,
                                   Properties prop)
                            throws UTGBShellException

Throws:

UTGBShellException

createFileFromTemplate

public static void createFileFromTemplate(Class<?> baseClass,
                                          String templateFilePath,
                                          String projectFolder,
                                          String relativePathOfTarget,
                                          Properties prop,
                                          boolean overWrite)
                                   throws UTGBShellException

Throws:

UTGBShellException