RuntimeParamUtil

java.lang.Object
- biolockj.util.RuntimeParamUtil

```
public class RuntimeParamUtil
extends Object
```
This utility processes the application runtime parameters passed to BioLockJ.

Field Summary

Fields
Modifier and Type	Field and Description
`protected static String`	`BASE_DIR_FLAG` Pipeline parent directory file-path runtime parameter switch: "b"
`protected static String`	`CONFIG_DIR_FLAG` `Config` file directory path runtime parameter switch: "C"
`protected static String`	`CONFIG_FLAG` `Config` file path runtime parameter switch: "c"
`protected static String`	`DIRECT_FLAG` Direct mode runtime parameter switch: "d"
`protected static String`	`DOCKER_FLAG` Docker mode runtime parameter switch: "-docker"
`protected static String`	`HOST_BLJ` Host BioLockJ deployment to run - used to override installed $BLJ in Docker containers with BioLockJ installed: "-blj"
`protected static String`	`HOST_BLJ_SUP` Host BioLockJ deployment to run - used to map $BLJ_SUP volume in Docker containers with BioLockJ installed: "-bljSup"
`protected static String`	`HOST_HOME_USER_DIR` Host $USER $HOME param: "u"
`protected static String`	`INPUT_DIR_FLAG` Input directory file-path runtime parameter switch: "i"
`protected static String`	`META_DIR_FLAG` Metadata file directory path runtime parameter switch: "m"
`protected static String`	`PASSWORD_FLAG` Change password runtime parameter switch: "p"
`protected static String`	`RESTART_FLAG` Restart pipeline runtime parameter switch: "r"

Constructor Summary

Constructors
Constructor and Description

RuntimeParamUtil()

Constructors
Constructor and Description
`RuntimeParamUtil()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`doChangePassword()` Return TRUE if runtime parameters indicate change password request
`static boolean`	`doRestart()` Return TRUE if runtime parameters indicate attempt to restart pipeline
`static String`	`getAdminEmailPassword()` Runtime property getter for "p"
`static File`	`getBaseDir()` Runtime property getter for "b"
`static String`	`getBaseDirParam()` Get the baseDir param and value
`static File`	`getConfigFile()` Runtime property getter for "c"
`static String`	`getConfigFileParam()` Used to build Docker run commands.
`static String`	`getDirectModuleDir()` Runtime property getter for "d"
`static String`	`getDirectModuleParam(BioModule module)` Direct module parameters contain 2 parts separated by a colon: (pipeline directory name):(module name)
`static File`	`getDirectPipelineDir()` Runtime property getter for direct module pipeline directory
`static File`	`getDockerHostBLJ_SUP()` Runtime property getter for Docker host blj_support dir
`static File`	`getDockerHostBLJ()` Runtime property getter for Docker host BioLockJ dir
`static String`	`getDockerHostConfigDir()` Runtime property getter for "C"
`static File`	`getDockerHostHomeUserDir()` Runtime property getter for Docker host $USER $HOME dir
`static String`	`getDockerHostInputDir()` Runtime property getter for "i"
`static String`	`getDockerHostMetaDir()` Runtime property getter for "m"
`static String`	`getDockerHostPipelineDir()` Runtime property getter for Docker host pipeline dir
`static String`	`getDockerJavaModuleParams()` Get Docker runtime arguments passed to BioLockJ from dockblj script. These are used to to populate BLJ_OPTIONS in Docker java_module scripts.
`static String`	`getProjectName()` Extract the project name from the Config file.
`static File`	`getRestartDir()` Return restart pipeline directory
`static boolean`	`isDockerMode()` Return TRUE if runtime parameter "-docker" was found
`static void`	`printRuntimeArgs(String[] args, boolean useSysOut)` Print the runtime args to System.out or using the Logger based on useSysOut parameter.
`static void`	`registerRuntimeParameters(String[] args)` Register and verify the runtime parameters.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - BASE_DIR_FLAG
```
protected static final String BASE_DIR_FLAG
```
    Pipeline parent directory file-path runtime parameter switch: "b"
    
    See Also:
    
    Constant Field Values
  - CONFIG_DIR_FLAG
```
protected static final String CONFIG_DIR_FLAG
```
    Config file directory path runtime parameter switch: "C"
    
    See Also:
    
    Constant Field Values
  - CONFIG_FLAG
```
protected static final String CONFIG_FLAG
```
    Config file path runtime parameter switch: "c"
    
    See Also:
    
    Constant Field Values
  - DIRECT_FLAG
```
protected static final String DIRECT_FLAG
```
    Direct mode runtime parameter switch: "d"
    
    See Also:
    
    Constant Field Values
  - DOCKER_FLAG
```
protected static final String DOCKER_FLAG
```
    Docker mode runtime parameter switch: "-docker"
    
    See Also:
    
    Constant Field Values
  - HOST_BLJ
```
protected static final String HOST_BLJ
```
    Host BioLockJ deployment to run - used to override installed $BLJ in Docker containers with BioLockJ installed: "-blj"
    
    See Also:
    
    Constant Field Values
  - HOST_BLJ_SUP
```
protected static final String HOST_BLJ_SUP
```
    Host BioLockJ deployment to run - used to map $BLJ_SUP volume in Docker containers with BioLockJ installed: "-bljSup"
    
    See Also:
    
    Constant Field Values
  - HOST_HOME_USER_DIR
```
protected static final String HOST_HOME_USER_DIR
```
    Host $USER $HOME param: "u"
    
    See Also:
    
    Constant Field Values
  - INPUT_DIR_FLAG
```
protected static final String INPUT_DIR_FLAG
```
    Input directory file-path runtime parameter switch: "i"
    
    See Also:
    
    Constant Field Values
  - META_DIR_FLAG
```
protected static final String META_DIR_FLAG
```
    Metadata file directory path runtime parameter switch: "m"
    
    See Also:
    
    Constant Field Values
  - PASSWORD_FLAG
```
protected static final String PASSWORD_FLAG
```
    Change password runtime parameter switch: "p"
    
    See Also:
    
    Constant Field Values
  - RESTART_FLAG
```
protected static final String RESTART_FLAG
```
    Restart pipeline runtime parameter switch: "r"
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - RuntimeParamUtil
```
public RuntimeParamUtil()
```
- Method Detail
  - doChangePassword
```
public static boolean doChangePassword()
```
    Return TRUE if runtime parameters indicate change password request
    
    Returns:
    
    boolean
  - doRestart
```
public static boolean doRestart()
```
    Return TRUE if runtime parameters indicate attempt to restart pipeline
    
    Returns:
    
    boolean
  - getAdminEmailPassword
```
public static String getAdminEmailPassword()
```
    Runtime property getter for "p"
    
    Returns:
    
    New clear-text password
  - getBaseDir
```
public static File getBaseDir()
```
    Runtime property getter for "b"
    
    Returns:
    
    $BLJ_PROJ pipeline parent directory
  - getBaseDirParam
```
public static String getBaseDirParam()
```
    Get the baseDir param and value
    
    Returns:
    
    String baseDir param and value
  - getConfigFile
```
public static File getConfigFile()
```
    Runtime property getter for "c"
    
    Returns:
    
    Config file
  - getConfigFileParam
```
public static String getConfigFileParam()
```
    Used to build Docker run commands.
    
    Returns:
    
    Config file param and value.
  - getDirectModuleDir
```
public static String getDirectModuleDir()
```
    Runtime property getter for "d"
    
    Returns:
    
    Direct module BioModule class name
  - getDirectModuleParam
```
public static String getDirectModuleParam(BioModule module)
```
    Direct module parameters contain 2 parts separated by a colon: (pipeline directory name):(module name)
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    Direct parameter flag + value
  - getDirectPipelineDir
```
public static File getDirectPipelineDir()
```
    Runtime property getter for direct module pipeline directory
    
    Returns:
    
    Pipeline directory dir
  - getDockerHostBLJ
```
public static File getDockerHostBLJ()
```
    Runtime property getter for Docker host BioLockJ dir
    
    Returns:
    
    Host "-blj" directory
  - getDockerHostBLJ_SUP
```
public static File getDockerHostBLJ_SUP()
```
    Runtime property getter for Docker host blj_support dir
    
    Returns:
    
    Host "-bljSup" directory
  - getDockerHostConfigDir
```
public static String getDockerHostConfigDir()
```
    Runtime property getter for "C"
    
    Returns:
    
    PCR primer file directory path
  - getDockerHostHomeUserDir
```
public static File getDockerHostHomeUserDir()
```
    Runtime property getter for Docker host $USER $HOME dir
    
    Returns:
    
    Host "u" directory
  - getDockerHostInputDir
```
public static String getDockerHostInputDir()
```
    Runtime property getter for "i"
    
    Returns:
    
    Host "input.dirPaths" directory
  - getDockerHostMetaDir
```
public static String getDockerHostMetaDir()
```
    Runtime property getter for "m"
    
    Returns:
    
    Metadata file directory path
  - getDockerHostPipelineDir
```
public static String getDockerHostPipelineDir()
```
    Runtime property getter for Docker host pipeline dir
    
    Returns:
    
    Host "internal.pipelineDir" directory
  - getDockerJavaModuleParams
```
public static String getDockerJavaModuleParams()
```
    Get Docker runtime arguments passed to BioLockJ from dockblj script.
    These are used to to populate BLJ_OPTIONS in Docker java_module scripts.
    
    Returns:
    
    Docker runtime parameters
  - getProjectName
```
public static String getProjectName()
```
    Extract the project name from the Config file.
    
    Returns:
    
    Project name
  - getRestartDir
```
public static File getRestartDir()
```
    Return restart pipeline directory
    
    Returns:
    
    File directory path
  - isDockerMode
```
public static boolean isDockerMode()
```
    Return TRUE if runtime parameter "-docker" was found
    
    Returns:
    
    boolean
  - printRuntimeArgs
```
public static void printRuntimeArgs(String[] args,
                                    boolean useSysOut)
```
    Print the runtime args to System.out or using the Logger based on useSysOut parameter.
    
    Parameters:
    
    args - Runtime Args
    
    useSysOut - Set TRUE if should use System.out to print
  - registerRuntimeParameters
```
public static void registerRuntimeParameters(String[] args)
                                      throws Exception
```
    Register and verify the runtime parameters. There are 2 required parameters:
    1. The Config file path
    2. The pipeline parent directory ($DOCKER_PROJ)
    Parameters:
    
    args - Program runtime parameters
    
    Throws:
    
    Exception - if invalid parameters detected

Class RuntimeParamUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BASE_DIR_FLAG

CONFIG_DIR_FLAG

CONFIG_FLAG

DIRECT_FLAG

DOCKER_FLAG

HOST_BLJ

HOST_BLJ_SUP

HOST_HOME_USER_DIR

INPUT_DIR_FLAG

META_DIR_FLAG

PASSWORD_FLAG

RESTART_FLAG

Constructor Detail

RuntimeParamUtil

Method Detail

doChangePassword

doRestart

getAdminEmailPassword

getBaseDir

getBaseDirParam

getConfigFile

getConfigFileParam

getDirectModuleDir

getDirectModuleParam

getDirectPipelineDir

getDockerHostBLJ

getDockerHostBLJ_SUP

getDockerHostConfigDir

getDockerHostHomeUserDir

getDockerHostInputDir

getDockerHostMetaDir

getDockerHostPipelineDir

getDockerJavaModuleParams

getProjectName

getRestartDir

isDockerMode

printRuntimeArgs

registerRuntimeParameters