BioLockJ

java.lang.Object
- biolockj.BioLockJ

```
public class BioLockJ
extends Object
```
This is the primary BioLockJ class - its main() method is executed when the jar is run.
This class validates the runtime parameters to run a new pipeline or restart a failed pipeline.
The Java log file is initialized and the configuration file is processed before starting the pipeline.
If the pipeline is successful, the program executes clean up operations (if configured) and creates a status-complete indicator file in the pipeline root directory.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`copyFileToPipelineRoot(File file)` Copy file to pipeline root directory.
`protected static void`	`copyInputData()` Create a copy of the sequence files in property "input.dirPaths", output to a directory named "internal.pipelineDir"/input.
`protected static File`	`createPipelineDirectory()` Create the pipeline root directory under $DOCKER_PROJ and save the path to `Config`."internal.pipelineDir".
`static String`	`getHelpInfo(File errFile)` Print error file path, restart instructions, and link to the BioLockJ Wiki
`protected static void`	`initBioLockJ(String[] args)` Execution summary: Call `MemoryUtil.reportMemoryUsage(String)` for baseline memory info Call `RuntimeParamUtil.registerRuntimeParameters(String[])` Call `MetaUtil.initialize()` to verify metadata dependencies Call `Config.initialize()` to create pipeline root dir and load properties Initialize `Log` with /resources/log4J.properties Copy initial metadata file into the pipeline root directory Call `SeqUtil.initialize()` to set Config parameters based on sequence files
`protected static void`	`initRestart()` Initialize restarted pipeline by: Initialize `Log` file using the name of the pipeline root directory Update summary #Attempts count Delete status file "biolockjFailed" in pipeline root directory If pipeline status = "biolockjComplete" Delete file "downloadList.txt" in pipeline root directory
`static boolean`	`isPipelineComplete()` Determine project status based on existence of "biolockjComplete" in pipeline root directory.
`static void`	`main(String[] args)` `BioLockJ` is the BioLockj.jar Main-Class, and is the first method executed. Execution summary: Call `initBioLockJ(String[])` to assign pipeline root dir and log file If change password pipeline, call `Email.encryptAndStoreEmailPassword()` Otherwise execute `runPipeline()`
`protected static void`	`markProjectStatus(String status)` Create indicator file in pipeline root directory, with name = status parameter.
`static File`	`pipelineInputDir()` Return the pipeline input directory
`protected static void`	`removeTempFiles()` Delete all `BioModule`/"temp" folders.
`protected static void`	`runPipeline()` Execution summary: Call `Pipeline.initializePipeline()` to initialize Pipeline modules For direct module execution call `Pipeline.runDirectModule(Integer)` Otherwise execute `Pipeline.startPipeline()` and save MASTER `Config` If `Config`."pipeline.deleteTempFiles" = "Y", Call `removeTempFiles()` to delete temp files Call `markProjectStatus(String)` to set the overall pipeline status as successful

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

- Method Detail
  - copyFileToPipelineRoot
```
public static void copyFileToPipelineRoot(File file)
                                   throws Exception
```
    Copy file to pipeline root directory.
    
    Parameters:
    
    file - File to copy
    
    Throws:
    
    Exception - if errors occur
  - getHelpInfo
```
public static String getHelpInfo(File errFile)
```
    Print error file path, restart instructions, and link to the BioLockJ Wiki
    
    Parameters:
    
    errFile - Error File
    
    Returns:
    
    Help Info
  - isPipelineComplete
```
public static boolean isPipelineComplete()
```
    Determine project status based on existence of "biolockjComplete" in pipeline root directory.
    
    Returns:
    
    true if "biolockjComplete" exists in the pipeline root directory, otherwise false
  - main
```
public static void main(String[] args)
```
    BioLockJ is the BioLockj.jar Main-Class, and is the first method executed.
    Execution summary:
    1. Call initBioLockJ(String[]) to assign pipeline root dir and log file
    2. If change password pipeline, call Email.encryptAndStoreEmailPassword()
    3. Otherwise execute runPipeline()
    If pipeline has failed, attempt execute Email (if configured) to notify user of failures.
    Parameters:
    
    args - - String[] runtime parameters passed to the Java program when launching BioLockJ
  - pipelineInputDir
```
public static File pipelineInputDir()
```
    Return the pipeline input directory
    
    Returns:
    
    Input dir
  - copyInputData
```
protected static void copyInputData()
                             throws Exception
```
    Create a copy of the sequence files in property "input.dirPaths", output to a directory named "internal.pipelineDir"/input.
    
    Throws:
    
    Exception - if unable to copy the files
  - createPipelineDirectory
```
protected static File createPipelineDirectory()
```
    Create the pipeline root directory under $DOCKER_PROJ and save the path to Config."internal.pipelineDir".
    For example, the following Config settings will create: /projects/MicrobeProj_2018Jan01
    - $DOCKER_PROJ = /projects
    - Config file name = MicrobeProj.properties
    - Current date = January 1, 2018
    Returns:
    
    Pipeline root directory
  - initBioLockJ
```
protected static void initBioLockJ(String[] args)
                            throws Exception
```
    Execution summary:
    1. Call MemoryUtil.reportMemoryUsage(String) for baseline memory info
    2. Call RuntimeParamUtil.registerRuntimeParameters(String[])
    3. Call MetaUtil.initialize() to verify metadata dependencies
    4. Call Config.initialize() to create pipeline root dir and load properties
    5. Initialize Log with /resources/log4J.properties
    6. Copy initial metadata file into the pipeline root directory
    7. Call SeqUtil.initialize() to set Config parameters based on sequence files
    Parameters:
    
    args - - String[] runtime parameters passed to the Java program when launching BioLockJ
    
    Throws:
    
    Exception - if errors occur
  - initRestart
```
protected static void initRestart()
                           throws Exception
```
    Initialize restarted pipeline by:
    1. Initialize Log file using the name of the pipeline root directory
    2. Update summary #Attempts count
    3. Delete status file "biolockjFailed" in pipeline root directory
    4. If pipeline status = "biolockjComplete"
    5. Delete file "downloadList.txt" in pipeline root directory
    Throws:
    
    Exception - if errors occur
  - markProjectStatus
```
protected static void markProjectStatus(String status)
```
    Create indicator file in pipeline root directory, with name = status parameter. Config."internal.pipelineDir".
    
    Parameters:
    
    status - Status indicator file name
  - removeTempFiles
```
protected static void removeTempFiles()
                               throws Exception
```
    Delete all BioModule/"temp" folders.
    
    Throws:
    
    Exception - if unable to delete temp files
  - runPipeline
```
protected static void runPipeline()
                           throws Exception
```
    Execution summary:
    1. Call Pipeline.initializePipeline() to initialize Pipeline modules
    2. For direct module execution call Pipeline.runDirectModule(Integer)
    3. Otherwise execute Pipeline.startPipeline() and save MASTER Config
    4. If Config."pipeline.deleteTempFiles" = "Y", Call removeTempFiles() to delete temp files
    5. Call markProjectStatus(String) to set the overall pipeline status as successful
    Throws:
    
    Exception - if runtime errors occur

Class BioLockJ

Method Summary

Methods inherited from class java.lang.Object

Method Detail

copyFileToPipelineRoot

getHelpInfo

isPipelineComplete

main

pipelineInputDir

copyInputData

createPipelineDirectory

initBioLockJ

initRestart

markProjectStatus

removeTempFiles

runPipeline