BashScriptBuilder

java.lang.Object
- biolockj.util.BashScriptBuilder

```
public class BashScriptBuilder
extends Object
```
This utility class generates the bash script files using the lines provided and Config script properties.

Field Summary

Fields
Modifier and Type	Field and Description
`protected static String`	`CLUSTER_BATCH_COMMAND` `Config` String property: "cluster.batchCommand" Terminal command used to submit jobs on the cluster.
`protected static String`	`CLUSTER_MODULES` `Config` List property: "cluster.modules" List of cluster modules to load at start of worker scripts.
`protected static List<String>`	`CLUSTER_NUM_PROCESSORS` One parameter of the `Config` String property "cluster.jobHeader" to set number of cores.
`protected static String`	`CLUSTER_PROLOGUE` `Config` String property: "cluster.prologue" To run at the start of every script after loading cluster modules (if any)
`protected static String`	`CLUSTER_VALIDATE_PARAMS` `Config` Boolean property: "cluster.validateParams" If set to "Y", validate "cluster.jobHeader" param cluster number of processors = "script.numThreads" or `ScriptModule.SCRIPT_NUM_THREADS`
`protected static String`	`FUNCTION_EXECUTE` Worker script function to execute 1 line of a worker script.
`protected static String`	`FUNCTION_RUN_JOB` Main script function to submit jobs on the cluster
`protected static String`	`SCRIPT_JOB_HEADER` `Config` String property: "cluster.jobHeader" Header written at top of worker scripts

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`protected static List<String>`	`buildExecuteFunction(String script)` Create bash worker script function: "execute". Failure details written to the failure script file if any occur.
`static void`	`buildMainScript(ScriptModule module)` Build the MIAN script.
`static void`	`buildScripts(ScriptModule module, List<List<String>> data)` This method builds the bash scripts required for the given module. Standard local/cluster pipelines include: 1 MAIN script, 1+ worker-scripts. Docker R_Modules include: 1 MAIN scirpt, 0 worker-scripts - MAIN.R run by MAIN.sh Docker non-R_Modules include: 1 MAIN scirpt, 1+ worker-scripts - MAIN.sh runs workers AWS Docker R_Modules include: 0 MAIN scirpts, 0 worker-scripts - MAIN.R run by nextflow AWS Docker non-R_Modules include: 0 MAIN scirpts, 1+ worker-scripts MAIN.sh runs workers
`protected static File`	`createScript(String scriptPath, List<String> lines)` Create the script.
`protected static String`	`getMainScriptExecuteWorkerLine(ScriptModule module, String workerScriptPath, String workerId)` Call "execute" on the worker script
`protected static List<String>`	`getWorkerScriptLines(List<String> lines)` Pass each line and the current line number to "execute"
`protected static String`	`getWorkerScriptPath(ScriptModule module, String workerId)` Build the file path for the numbered worker script.
`protected static List<String>`	`initMainScript(ScriptModule module)` Create the ScriptModule main script that calls all worker scripts.
`protected static List<String>`	`initWorkerScript(ScriptModule module, String scriptPath)` Create the numbered worker scripts.
`protected static void`	`verifyConfig(ScriptModule module)` If property "pipeline.env" = cluster, require property "cluster.batchCommand", otherwise exit this method.
`protected static void`	`writeScript(BufferedWriter writer, List<String> lines)` This method formats the bash script to indent if statement code blocks

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

- Field Detail
  - CLUSTER_BATCH_COMMAND
```
protected static final String CLUSTER_BATCH_COMMAND
```
    Config String property: "cluster.batchCommand"
    Terminal command used to submit jobs on the cluster.
    
    See Also:
    
    Constant Field Values
  - CLUSTER_MODULES
```
protected static final String CLUSTER_MODULES
```
    Config List property: "cluster.modules"
    List of cluster modules to load at start of worker scripts.
    
    See Also:
    
    Constant Field Values
  - CLUSTER_NUM_PROCESSORS
```
protected static final List<String> CLUSTER_NUM_PROCESSORS
```
    One parameter of the Config String property "cluster.jobHeader" to set number of cores.
  - CLUSTER_PROLOGUE
```
protected static final String CLUSTER_PROLOGUE
```
    Config String property: "cluster.prologue"
    To run at the start of every script after loading cluster modules (if any)
    
    See Also:
    
    Constant Field Values
  - CLUSTER_VALIDATE_PARAMS
```
protected static final String CLUSTER_VALIDATE_PARAMS
```
    Config Boolean property: "cluster.validateParams"
    If set to "Y", validate "cluster.jobHeader" param cluster number of processors = "script.numThreads" or ScriptModule.SCRIPT_NUM_THREADS
    
    See Also:
    
    Constant Field Values
  - FUNCTION_EXECUTE
```
protected static final String FUNCTION_EXECUTE
```
    Worker script function to execute 1 line of a worker script.
    
    See Also:
    
    Constant Field Values
  - FUNCTION_RUN_JOB
```
protected static final String FUNCTION_RUN_JOB
```
    Main script function to submit jobs on the cluster
    
    See Also:
    
    Constant Field Values
  - SCRIPT_JOB_HEADER
```
protected static final String SCRIPT_JOB_HEADER
```
    Config String property: "cluster.jobHeader"
    Header written at top of worker scripts
    
    See Also:
    
    Constant Field Values
- Method Detail
  - buildMainScript
```
public static void buildMainScript(ScriptModule module)
                            throws Exception
```
    Build the MIAN script.
    
    Parameters:
    
    module - ScriptModule
    
    Throws:
    
    Exception - if any error occurs
  - buildScripts
```
public static void buildScripts(ScriptModule module,
                                List<List<String>> data)
                         throws Exception
```
    This method builds the bash scripts required for the given module.
    Standard local/cluster pipelines include: 1 MAIN script, 1+ worker-scripts.
    Docker R_Modules include: 1 MAIN scirpt, 0 worker-scripts - MAIN.R run by MAIN.sh
    Docker *non-R_Modules* include: 1 MAIN scirpt, 1+ worker-scripts - MAIN.sh runs workers
    AWS Docker R_Modules include: 0 MAIN scirpts, 0 worker-scripts - MAIN.R run by nextflow
    AWS Docker *non-R_Modules* include: 0 MAIN scirpts, 1+ worker-scripts MAIN.sh runs workers
    
    Parameters:
    
    module - ScriptModule
    
    data - Bash script lines
    
    Throws:
    
    Exception - if any error occurs
  - buildExecuteFunction
```
protected static List<String> buildExecuteFunction(String script)
```
    Create bash worker script function: "execute".
    Failure details written to the failure script file if any occur.
    1. $1 Script payload line to execute
    2. $2 Script line number
    Parameters:
    
    script - Execute script
    
    Returns:
    
    Bash script lines
  - createScript
```
protected static File createScript(String scriptPath,
                                   List<String> lines)
                            throws Exception
```
    Create the script. Leading zeros added if needed so all worker scripts have same number of digits. Print the worker script as DEBUG to the log file.
    
    Parameters:
    
    scriptPath - Worker script path
    
    lines - Ordered bash script lines to write to the scriptPath
    
    Returns:
    
    File bash script
    
    Throws:
    
    Exception - if I/O errors occur
  - getMainScriptExecuteWorkerLine
```
protected static String getMainScriptExecuteWorkerLine(ScriptModule module,
                                                       String workerScriptPath,
                                                       String workerId)
```
    Call "execute" on the worker script
    
    Parameters:
    
    module - ScriptModule
    
    workerScriptPath - Worker script path
    
    workerId - Worker script ID
    
    Returns:
    
    bash script line
  - getWorkerScriptLines
```
protected static List<String> getWorkerScriptLines(List<String> lines)
```
    Pass each line and the current line number to "execute"
    
    Parameters:
    
    lines - Basic script lines generated by a BioModule.
    
    Returns:
    
    List of bash script lines
  - getWorkerScriptPath
```
protected static String getWorkerScriptPath(ScriptModule module,
                                            String workerId)
                                     throws Exception
```
    Build the file path for the numbered worker script. Leading zeros added if needed so all worker scripts have same number of digits.
    
    Parameters:
    
    module - ScriptModule is the module that owns the scripts
    
    workerId - Worker ID
    
    Returns:
    
    Absolute path of next worker script
    
    Throws:
    
    Exception - if I/O errors occur
  - initMainScript
```
protected static List<String> initMainScript(ScriptModule module)
                                      throws Exception
```
    Create the ScriptModule main script that calls all worker scripts.
    
    Parameters:
    
    module - ScriptModule script directory is where main script is written
    
    Returns:
    
    List of lines for the main script that has the prefix
    
    Throws:
    
    Exception - if error occurs writing the file
  - initWorkerScript
```
protected static List<String> initWorkerScript(ScriptModule module,
                                               String scriptPath)
                                        throws Exception
```
    Create the numbered worker scripts. Leading zeros added if needed so all worker scripts names are the same length. If run on cluster and cluster.jobHeader is defined, add cluster.jobHeader as header for worker scripts. Otherwise, use the same script.defaultHeader as used in the MAIN script.
    
    Parameters:
    
    module - ScriptModule script directory is where main script is written
    
    scriptPath - Worker script absolute file path
    
    Returns:
    
    Lines for the worker script
    
    Throws:
    
    Exception - if required properties are undefined
  - verifyConfig
```
protected static void verifyConfig(ScriptModule module)
                            throws Exception
```
    If property "pipeline.env" = cluster, require property "cluster.batchCommand", otherwise exit this method.
    If running on the cluster and property "cluster.validateParams" = "Y":
    1. Require property "cluster.jobHeader"
    2. Require property "cluster.batchCommand" sets #cores param (ppn or procs) = ScriptModule.SCRIPT_NUM_THREADS or
    Current format #1 (2018) for UNCC HPC Cluster: #PBS -l procs=1,mem=8GB,walltime=8:00:00
    Current format #2 (2018) for UNCC HPC Cluster: #PBS -l ppn=1,mem=8GB,walltime=8:00:00
    Parameters:
    
    module - ScriptModuel
    
    Throws:
    
    Exception - if any validation fails
  - writeScript
```
protected static void writeScript(BufferedWriter writer,
                                  List<String> lines)
                           throws Exception
```
    This method formats the bash script to indent if statement code blocks
    
    Parameters:
    
    writer - BufferedWriter writes to the file
    
    lines - List or shell script lines
    
    Throws:
    
    Exception - if I/O errors occur

Class BashScriptBuilder

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CLUSTER_BATCH_COMMAND

CLUSTER_MODULES

CLUSTER_NUM_PROCESSORS

CLUSTER_PROLOGUE

CLUSTER_VALIDATE_PARAMS

FUNCTION_EXECUTE

FUNCTION_RUN_JOB

SCRIPT_JOB_HEADER

Method Detail

buildMainScript

buildScripts

buildExecuteFunction

createScript

getMainScriptExecuteWorkerLine

getWorkerScriptLines

getWorkerScriptPath

initMainScript

initWorkerScript

verifyConfig

writeScript