biolockj.module

Class JavaModuleImpl

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

Demultiplexer, Humann2CountModule, JsonReport, Multiplexer, OtuCountModule, ParserModuleImpl, RarefySeqs, RdpHierParser, RegisterNumReads, SeqFileValidator, TaxaCountModule, TrimPrimers

public abstract class JavaModuleImpl
extends ScriptModuleImpl
implements JavaModule

Superclass for Java BioModules that will be called in separate instances of the application.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	BLJ_OPTIONS Docker environment variable holding the Docker program switches: "BLJ_OPTIONS"

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
JavaModuleImpl()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Java script only require 2 lines, one to run the blj_config to update our $PATH and gain access to environment variables, and then the direct call to the BioLockJ.jar.
void	executeTask() JavaModules run pure Java code. If in Direct mode, execute runModule() to run the module functionality; another BioLockJ instance is the manager that has launched this instance to run this module. Otherwise, this instance is the manager, If Config."pipeline.detachJavaModules"="Y" execute BioModule.executeTask() to build the bash scripts to launch a secondary instance in direct mode to run this module. Otherwise (if "pipeline.detachJavaModules"="N"), execute runModule() to run the Java code to execute module functionality within the manager instance.
String	getDockerImageName() Get the docker image to use for this module.
String	getDockerImageOwner() Get the name of the docker hub user that owns the image to use for this module.
String	getDockerImageTag() Get the version / tag to use for the docker image.
List<String>	getWorkerScriptFunctions() If in Docker mode, set "BLJ_OPTIONS" which will be reference in every worker script when running BioLockJ in direct mode.
boolean	isValidInputModule(BioModule module) If module is a SeqModule input must contain sequence data.
protected void	markStatus(String status) This method sets the module status by saving the indicator file to the module root dir.
void	moduleComplete() This method will create the success flag file so the next module can run.
void	moduleFailed() This method will create the fail flag file so the pipeline can move on..
protected String	runBioLockJ_CMD() Get the java command to launch a module directly.
abstract void	runModule() This method executes the modules primary Java routine.

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias, version

Field Detail

BLJ_OPTIONS

protected static final String BLJ_OPTIONS

Docker environment variable holding the Docker program switches: "BLJ_OPTIONS"

See Also:

Constant Field Values

Constructor Detail

JavaModuleImpl

public JavaModuleImpl()

Method Detail

buildScript

public List<List<String>> buildScript(List<File> files)
                               throws Exception

Java script only require 2 lines, one to run the blj_config to update our $PATH and gain access to environment variables, and then the direct call to the BioLockJ.jar.

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - Files in the input directory that contain only forward reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate script lines

executeTask

public void executeTask()
                 throws Exception

JavaModules run pure Java code.
If in Direct mode, execute runModule() to run the module functionality; another BioLockJ instance is the manager that has launched this instance to run this module.
Otherwise, this instance is the manager,
If Config."pipeline.detachJavaModules"="Y" execute BioModule.executeTask() to build the bash scripts to launch a secondary instance in direct mode to run this module.
Otherwise (if "pipeline.detachJavaModules"="N"), execute runModule() to run the Java code to execute module functionality within the manager instance.

Specified by:

executeTask in interface BioModule

Overrides:

executeTask in class ScriptModuleImpl

Throws:

Exception - thrown if the module is unable to complete is task

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

If in Docker mode, set "BLJ_OPTIONS" which will be reference in every worker script when running BioLockJ in direct mode.

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

isValidInputModule

public boolean isValidInputModule(BioModule module)

If module is a SeqModule input must contain sequence data.

Specified by:

isValidInputModule in interface BioModule

Overrides:

isValidInputModule in class BioModuleImpl

Parameters:

module - BioModule that ran before the current BioModule

Returns:

boolean TRUE if the previousModule output is acceptable input for the current BioModule

moduleComplete

public void moduleComplete()
                    throws Exception

Description copied from interface: JavaModule

This method will create the success flag file so the next module can run.

Specified by:

moduleComplete in interface JavaModule

Throws:

Exception - thrown if any runtime error occurs

moduleFailed

public void moduleFailed()
                  throws Exception

Description copied from interface: JavaModule

This method will create the fail flag file so the pipeline can move on..

Specified by:

moduleFailed in interface JavaModule

Throws:

Exception - thrown if any runtime error occurs

runModule

public abstract void runModule()
                        throws Exception

Description copied from interface: JavaModule

This method executes the modules primary Java routine.

Specified by:

runModule in interface JavaModule

Throws:

Exception - thrown if any runtime error occurs

markStatus

protected void markStatus(String status)
                   throws Exception

This method sets the module status by saving the indicator file to the module root dir.

Parameters:

status - Success or Failures

Throws:

Exception - if unable to set the status

runBioLockJ_CMD

protected final String runBioLockJ_CMD()

Get the java command to launch a module directly. The java command will be a repeat of the command originally used to launch the program, only the arguments to BioLockJ will be different; they are set in a different method. If any external modules were used in this pipeline, they should be added to the class path in the launch script. At this stage, the same class path used to launch the program is used for the module.

Returns:

java source parameter (either Jar or main class with class-path)

Throws:

Exception - if unable to determine source

getDockerImageOwner

public String getDockerImageOwner()

Description copied from interface: BioModule

Get the name of the docker hub user that owns the image to use for this module. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageOwner in interface BioModule

Overrides:

getDockerImageOwner in class BioModuleImpl

Returns:

getDockerImageName

public String getDockerImageName()

Description copied from interface: BioModule

Get the docker image to use for this module. The owner and version/tag are specificed separately; this is just the image name. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageName in interface BioModule

Returns:

getDockerImageTag

public String getDockerImageTag()

Description copied from interface: BioModule

Get the version / tag to use for the docker image. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageTag in interface BioModule

Overrides:

getDockerImageTag in class BioModuleImpl

Returns: