public class Pipeline extends Object
Modifier and Type | Method and Description |
---|---|
protected static boolean |
checkModuleDependencies()
Initialization occurs by calling
BioModule methods on configured modulesCreate 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" directoryCall refreshRCacheIfNeeded() to cache R fields after 1st R module runsVerify 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.
|
public static void executeModule() throws Exception
Exception
- if runtime errors occurpublic static BioModule exeModule()
public static List<BioModule> getModules()
BioModule
s constructed by the BioModuleFactory
public static String getStatus()
public static void initializePipeline() throws Exception
Exception
- if errors occurpublic static void runDirectModule(Integer id) throws Exception
id
- Module IDException
- if errors occurpublic static void runPipeline() throws Exception
Exception
- if any fatal error occurs during executionprotected static void executeModules() throws Exception
BioModule
s are run in the order listed in the Config
file.Execution steps:
Exception
- if script errors occurprotected static boolean checkModuleDependencies() throws Exception
BioModule
methods on configured modulesConfig
file.SummaryUtil
module so previous summary descriptions can be used for completed
modules
refreshRCacheIfNeeded()
to cache R fields after 1st R module runsBioModule.checkDependencies()
Exception
- thrown if propagated by called methodsprotected static void checkOneModulesDependencies(BioModule module) throws Exception
Exception
protected static boolean poll(ScriptModule module) throws Exception
ScriptModule.getScriptDir()
will contain one main script and one ore more worker
scripts.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.module
- ScriptModuleException
- thrown to end pipeline execution