Pipeline

java.lang.Object
- biolockj.Pipeline

```
public class Pipeline
extends Object
```
This class initializes and executes each BioModule configured for execution.
BioModules that generate scripts are monitored until all scripts are complete, before moving on to the next module.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`protected static boolean`	`checkModuleDependencies()` Initialization occurs by calling `BioModule` methods on configured modules Create module sub-directories under "internal.pipelineDir" as ordered in `Config` file. Reset the `SummaryUtil` module so previous summary descriptions can be used for completed modules Delete incomplete module contents if restarting a failed pipeline "output" directory Call `refreshRCacheIfNeeded()` to cache R fields after 1st R module runs Verify dependencies with `BioModule.checkDependencies()`
`protected static void`	`checkOneModulesDependencies(BioModule module)`
`static void`	`executeModule()` Execute a single pipeline module.
`protected static void`	`executeModules()` This method executes all new and incomplete modules Before/after a module is executed, set persistent module status by creating status indicator files.
`static BioModule`	`exeModule()` Return the BioModule currently being executed
`static List<BioModule>`	`getModules()` Return a list of `BioModule`s constructed by the `BioModuleFactory`
`static String`	`getStatus()` Return if no pipelineException has been thrown, otherwise return FAILED
`static void`	`initializePipeline()` This method initializes the Pipeline by building the modules and checking module dependencies.
`protected static boolean`	`poll(ScriptModule module)` The `ScriptModule.getScriptDir()` will contain one main script and one ore more worker scripts. An empty file with appended to the script name is created when execution begins. If successful, an empty file with appended to the script name is created. Upon failure, an empty file with appended to the script name is created. Script status is polled each minute, determining status by counting indicator files. `Log` outputs the # of started, failed, and successful scripts (if any change). `Log` repeats the previous message every 10 minutes if no status change is detected.
`protected static void`	`refreshRCacheIfNeeded()` Refresh R cache if about to run the 1st R module.
`static void`	`runDirectModule(Integer id)` If moduleName is null, run all modules, otherwise only run the specified module.
`static void`	`runPipeline()` This method initializes and executes the BioModules set in the BioLockJ configuration file.

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

- Method Detail
  - executeModule
```
public static void executeModule()
                          throws Exception
```
    Execute a single pipeline module.
    
    Throws:
    
    Exception - if runtime errors occur
  - exeModule
```
public static BioModule exeModule()
```
    Return the BioModule currently being executed
    
    Returns:
    
    Current BioModule
  - getModules
```
public static List<BioModule> getModules()
```
    Return a list of BioModules constructed by the BioModuleFactory
    
    Returns:
    
    List of BioModules
  - getStatus
```
public static String getStatus()
```
    Return if no pipelineException has been thrown, otherwise return FAILED
    
    Returns:
    
    pipeline status (SUCCESS or FAILED)
  - initializePipeline
```
public static void initializePipeline()
                               throws Exception
```
    This method initializes the Pipeline by building the modules and checking module dependencies.
    
    Throws:
    
    Exception - if errors occur
  - runDirectModule
```
public static void runDirectModule(Integer id)
                            throws Exception
```
    If moduleName is null, run all modules, otherwise only run the specified module.
    
    Parameters:
    
    id - Module ID
    
    Throws:
    
    Exception - if errors occur
  - runPipeline
```
public static void runPipeline()
                        throws Exception
```
    This method initializes and executes the BioModules set in the BioLockJ configuration file.
    
    Throws:
    
    Exception - if any fatal error occurs during execution
  - executeModules
```
protected static void executeModules()
                              throws Exception
```
    This method executes all new and incomplete modules
    Before/after a module is executed, set persistent module status by creating status indicator files. Incomplete modules have an empty file in the module directory.
    Complete modules have an empty file in the module directory.
    BioModules are run in the order listed in the Config file.
    
    Execution steps:
    1. File is added to the module directory
    2. Run module scripts, if any, polling 1/minute for status until all scripts complete or time out.
    3. File is replaced by as status indicator
    Throws:
    
    Exception - if script errors occur
  - checkModuleDependencies
```
protected static boolean checkModuleDependencies()
                                          throws Exception
```
    Initialization occurs by calling BioModule methods on configured modules
    1. Create module sub-directories under "internal.pipelineDir" as ordered in Config file.
    2. Reset the SummaryUtil module so previous summary descriptions can be used for completed modules
    3. Delete incomplete module contents if restarting a failed pipeline "output" directory
    4. Call refreshRCacheIfNeeded() to cache R fields after 1st R module runs
    5. Verify dependencies with BioModule.checkDependencies()
    Returns:
    
    true if no errors are thrown
    
    Throws:
    
    Exception - thrown if propagated by called methods
  - checkOneModulesDependencies
```
protected static void checkOneModulesDependencies(BioModule module)
                                           throws Exception
```
    Throws:
    
    Exception
  - poll
```
protected static boolean poll(ScriptModule module)
                       throws Exception
```
    The ScriptModule.getScriptDir() will contain one main script and one ore more worker scripts.
    An empty file with appended to the script name is created when execution begins.
    If successful, an empty file with appended to the script name is created.
    Upon failure, an empty file with appended to the script name is created.
    Script status is polled each minute, determining status by counting indicator files.
    Log outputs the # of started, failed, and successful scripts (if any change).
    Log repeats the previous message every 10 minutes if no status change is detected.
    
    Parameters:
    
    module - ScriptModule
    
    Returns:
    
    true if all scripts are complete, regardless of status
    
    Throws:
    
    Exception - thrown to end pipeline execution
  - refreshRCacheIfNeeded
```
protected static void refreshRCacheIfNeeded()
                                     throws Exception
```
    Refresh R cache if about to run the 1st R module.
    
    Throws:
    
    Exception - if errors occur

Class Pipeline

Method Summary

Methods inherited from class java.lang.Object

Method Detail

executeModule

exeModule

getModules

getStatus

initializePipeline

runDirectModule

runPipeline

executeModules

checkModuleDependencies

checkOneModulesDependencies

poll

refreshRCacheIfNeeded