public class BioLockJ extends Object
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.
|
static String |
getHelpInfo()
Print error file path, restart instructions, and link to the BioLockJ Wiki
|
static File |
getPipelineDir() |
static String |
getPipelineId() |
static String |
getProjectName()
Extract the project name from the Config file.
|
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 |
removeTempFiles()
|
protected static void |
runPipeline()
Execution summary:
Call Pipeline.initializePipeline() to initialize Pipeline modules
For direct module execution call Pipeline.runDirectModule(Integer)
Otherwise execute Pipeline.runPipeline() and save MASTER Config
If Config ."pipeline.deleteTempFiles" = "Y", Call
removeTempFiles() to delete temp files
Call BioLockJUtil.createFile(String) to set the overall pipeline status as successful
|
public static void copyFileToPipelineRoot(File file) throws Exception
file
- File to copyException
- if errors occurpublic static String getHelpInfo()
public static boolean isPipelineComplete()
public static void main(String[] args)
BioLockJ
is the BioLockJ.jar Main-Class, and is the first method executed.initBioLockJ(String[])
to assign pipeline root dir and log file
Email.encryptAndStoreEmailPassword()
runPipeline()
If pipeline has failed, attempt execute Email
(if configured) to notify user of
failures.
args
- - String[] runtime parameters passed to the Java program when launching BioLockJprotected static void copyInputData() throws Exception
Exception
- if unable to copy the filesprotected static void initBioLockJ(String[] args) throws Exception
MemoryUtil.reportMemoryUsage(String)
for baseline memory info
RuntimeParamUtil.registerRuntimeParameters(String[])
MetaUtil.initialize()
to verify metadata dependencies
Config.initialize()
to create pipeline root dir and load properties
Log
with /resources/log4J.properties
SeqUtil.initialize()
to set Config parameters based on sequence files
args
- - String[] runtime parameters passed to the Java program when launching BioLockJException
- if errors occurprotected static void initRestart() throws Exception
Log
file using the name of the pipeline root directory
Exception
- if errors occurprotected static void removeTempFiles()
protected static void runPipeline() throws Exception
Pipeline.initializePipeline()
to initialize Pipeline modules
Pipeline.runDirectModule(Integer)
Pipeline.runPipeline()
and save MASTER Config
Config
."pipeline.deleteTempFiles" = "Y", Call
removeTempFiles()
to delete temp files
BioLockJUtil.createFile(String)
to set the overall pipeline status as successful
Exception
- if runtime errors occurpublic static String getProjectName() throws DockerVolCreationException
DockerVolCreationException
public static File getPipelineDir()
public static String getPipelineId()