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"
`protected static String`	`CLUSTER_HAS_BATCH_IDS` `Config` Boolean property: "cluster.returnsBatchIds"
`protected static String`	`CLUSTER_MODULES` `Config` List property: "cluster.modules"
`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"
`protected static String`	`CLUSTER_STATUS_COMMAND` `Config` String property: "cluster.statusCommand"
`protected static String`	`SCRIPT_JOB_HEADER` `Config` String property: "cluster.jobHeader"

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`protected static List<String>`	`buildExecuteFunction()` Create bash worker script function: executeLine Capture status code of the payload script line.
`protected static void`	`buildMainScript(ScriptModule module)` Build the MIAN script.
`protected static List<String>`	`buildScriptFailureFunction(String path)` Create bash worker script function: scriptFailed Failure details written to the failure indicator file: $1 Script payload line to execute $2 Script line number $3 Script line failure status code
`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 script, 0 worker-scripts - MAIN.R run by MAIN.sh Docker non-R_Modules include: 1 MAIN script, 1+ worker-scripts - MAIN.sh runs workers AWS Docker R_Modules include: 0 MAIN scripts, 0 worker-scripts - MAIN.R run by Nextflow AWS Docker non-R_Modules include: 0 MAIN scripts, 1+ worker-scripts MAIN.sh runs workers
`static void`	`checkDependencies(BioModule module)`
`protected static File`	`createScript(ScriptModule module, String scriptPath, List<String> lines)` Create the script.
`protected static String`	`getMainScriptExecuteWorkerLine(String workerScriptPath)` Call executeLine function in the worker script
`protected static List<String>`	`getWorkerScriptLines(List<String> lines)` Pass each line and the current line number to: executeLine
`protected static String`	`getWorkerScriptPath(ScriptModule module)` 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 List<String>`	`insertPathVars(ScriptModule module, List<String> scriptLines)` Paths to common module directories are added via `pathVariableVals`.
`static List<String>`	`listProps()` Let modules see property names.
`static List<String>`	`loadModules(ScriptModule module)` Return lines to script that load cluster modules based on `Config`."cluster.modules"
`protected static List<String>`	`passEnvironmentVarVals(ScriptModule module)`
`protected static List<String>`	`pathVariableVals(ScriptModule module)` Get the script lines to assign values to the common directories.
`static void`	`registerProps()` Register properties with the Properties class for API access.
`protected static void`	`writeScript(ScriptModule module, BufferedWriter writer, List<String> scriptLines)` 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"
    
    See Also:
    
    Constant Field Values
  - CLUSTER_HAS_BATCH_IDS
```
protected static final String CLUSTER_HAS_BATCH_IDS
```
    Config Boolean property: "cluster.returnsBatchIds"
    
    See Also:
    
    Constant Field Values
  - CLUSTER_STATUS_COMMAND
```
protected static final String CLUSTER_STATUS_COMMAND
```
    Config String property: "cluster.statusCommand"
    
    See Also:
    
    Constant Field Values
  - CLUSTER_MODULES
```
protected static final String CLUSTER_MODULES
```
    Config List property: "cluster.modules"
    
    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"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_JOB_HEADER
```
protected static final String SCRIPT_JOB_HEADER
```
    Config String property: "cluster.jobHeader"
    
    See Also:
    
    Constant Field Values
- Method Detail
  - buildScripts
```
public static void buildScripts(ScriptModule module,
                                List<List<String>> data)
                         throws PipelineScriptException
```
    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 script, 0 worker-scripts - MAIN.R run by MAIN.sh
    Docker *non-R_Modules* include: 1 MAIN script, 1+ worker-scripts - MAIN.sh runs workers
    AWS Docker R_Modules include: 0 MAIN scripts, 0 worker-scripts - MAIN.R run by Nextflow
    AWS Docker *non-R_Modules* include: 0 MAIN scripts, 1+ worker-scripts MAIN.sh runs workers
    
    Parameters:
    
    module - ScriptModule
    
    data - Bash script lines
    
    Throws:
    
    PipelineScriptException - if any errors occur writing module script
  - buildExecuteFunction
```
protected static List<String> buildExecuteFunction()
```
    Create bash worker script function: executeLine
    Capture status code of the payload script line. Call scriptFailed function to capture all failure info (if any occur).
    
    Returns:
    
    Bash script lines
  - buildMainScript
```
protected static void buildMainScript(ScriptModule module)
                               throws ConfigException,
                                      IOException,
                                      DockerVolCreationException
```
    Build the MIAN script.
    
    Parameters:
    
    module - ScriptModule
    
    Throws:
    
    IOException - if errors occur writing the MAIN script lines
    
    ConfigException - if problems occur accessing Config properties
    
    DockerVolCreationException
  - buildScriptFailureFunction
```
protected static List<String> buildScriptFailureFunction(String path)
```
    Create bash worker script function: scriptFailed
    Failure details written to the failure indicator file:
    1. $1 Script payload line to execute
    2. $2 Script line number
    3. $3 Script line failure status code
    Parameters:
    
    path - Script path
    
    Returns:
    
    Bash script lines
  - createScript
```
protected static File createScript(ScriptModule module,
                                   String scriptPath,
                                   List<String> lines)
                            throws IOException
```
    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:
    
    module - ScriptModule
    
    scriptPath - Worker script path
    
    lines - Ordered bash script lines to write to the scriptPath
    
    Returns:
    
    File bash script
    
    Throws:
    
    IOException - if unable to write the bash script to file system
  - getMainScriptExecuteWorkerLine
```
protected static String getMainScriptExecuteWorkerLine(String workerScriptPath)
```
    Call executeLine function in the worker script
    
    Parameters:
    
    workerScriptPath - Worker script path
    
    Returns:
    
    bash script line
  - getWorkerScriptLines
```
protected static List<String> getWorkerScriptLines(List<String> lines)
```
    Pass each line and the current line number to: executeLine
    
    Parameters:
    
    lines - Basic script lines generated by a BioModule.
    
    Returns:
    
    List of bash script lines
  - getWorkerScriptPath
```
protected static String getWorkerScriptPath(ScriptModule module)
                                     throws ConfigNotFoundException,
                                            ConfigFormatException
```
    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
    
    Returns:
    
    Absolute path of next worker script
    
    Throws:
    
    ConfigFormatException - if "script.numWorkers" property is not a positive integer
    
    ConfigNotFoundException - if "script.numWorkers" property is undefined
  - initMainScript
```
protected static List<String> initMainScript(ScriptModule module)
                                      throws ConfigException,
                                             DockerVolCreationException
```
    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:
    
    ConfigException - if errors occur accessing Config properties
    
    DockerVolCreationException
  - pathVariableVals
```
protected static List<String> pathVariableVals(ScriptModule module)
```
    Get the script lines to assign values to the common directories. Using these variables in place of full file paths makes the script easier to read. The scripts file paths are replaced with variables in insertPathVars.
    
    Parameters:
    
    module -
    
    Returns:
    
    See Also:
    
    insertPathVars
  - passEnvironmentVarVals
```
protected static List<String> passEnvironmentVarVals(ScriptModule module)
                                              throws ConfigNotFoundException,
                                                     ConfigFormatException
```
    Throws:
    
    ConfigNotFoundException
    
    ConfigFormatException
  - insertPathVars
```
protected static List<String> insertPathVars(ScriptModule module,
                                             List<String> scriptLines)
```
    Paths to common module directories are added via pathVariableVals. Using these variables in place of full file paths makes the script easier to read.
    
    Parameters:
    
    module -
    
    scriptLines -
    
    Returns:
    
    See Also:
    
    pathVariableVals
  - 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
  - writeScript
```
protected static void writeScript(ScriptModule module,
                                  BufferedWriter writer,
                                  List<String> scriptLines)
                           throws IOException
```
    This method formats the bash script to indent if statement code blocks
    
    Parameters:
    
    module - ScriptModule
    
    writer - BufferedWriter writes to the file
    
    scriptLines - List or shell script lines
    
    Throws:
    
    IOException - if errors occur writing the new script
  - loadModules
```
public static List<String> loadModules(ScriptModule module)
```
    Return lines to script that load cluster modules based on Config."cluster.modules"
    
    Parameters:
    
    module - ScriptModule
    
    Returns:
    
    Bash Script lines to load cluster modules
  - registerProps
```
public static void registerProps()
                          throws API_Exception
```
    Register properties with the Properties class for API access.
    
    Throws:
    
    API_Exception
  - listProps
```
public static List<String> listProps()
```
    Let modules see property names.
  - checkDependencies
```
public static void checkDependencies(BioModule module)
                              throws ConfigNotFoundException,
                                     ConfigFormatException
```
    Throws:
    
    ConfigNotFoundException
    
    ConfigFormatException

Class BashScriptBuilder

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CLUSTER_BATCH_COMMAND

CLUSTER_HAS_BATCH_IDS

CLUSTER_STATUS_COMMAND

CLUSTER_MODULES

CLUSTER_NUM_PROCESSORS

CLUSTER_PROLOGUE

SCRIPT_JOB_HEADER

Method Detail

buildScripts

buildExecuteFunction

buildMainScript

buildScriptFailureFunction

createScript

getMainScriptExecuteWorkerLine

getWorkerScriptLines

getWorkerScriptPath

initMainScript

pathVariableVals

passEnvironmentVarVals

insertPathVars

initWorkerScript

writeScript

loadModules

registerProps

listProps

checkDependencies