org.utgenome.shell
Class UTGBShellCommand

java.lang.Object
  extended by org.utgenome.core.cui.UTGBCommandBase
      extended by org.utgenome.shell.UTGBShellCommandBase
          extended by 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


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