biolockj.module.implicit.parser.r16s

Class RdpHierParser

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.implicit.parser.r16s.RdpHierParser

All Implemented Interfaces:

ApiModule, BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class RdpHierParser
extends JavaModuleImpl
implements ApiModule

Field Summary

Fields inherited from class biolockj.module.JavaModuleImpl

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
RdpHierParser()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Validate module dependencies: Require Config. exists Require Config. is positive integer Require Config. is positive integer Verify Config. is positive integer if set Start the AWS DB sync to S3 if a novel DB has been configure and "aws.copyDbToS3" is enabled
void	executeTask() JavaModules run pure Java code. If in Direct mode, execute JavaModuleImpl.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 JavaModuleImpl.runModule() to run the Java code to execute module functionality within the manager instance.
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
String	getDetails() A extension of getDescription.
List<File>	getInputFiles() BioModule BioModuleImpl.getInputFiles() is called to initialize upon first call and cached.
List<String>	getPreRequisiteModules() By default, no prerequisites are required.
boolean	isValidInputModule(BioModule module) If module is a SeqModule input must contain sequence data.
static void	main(String[] args) For stand-alone testing outside of a BioLockJ pipeline. arg 0 - comma-separated list of taxonomic levels arg 1 - comma-separated list of input files (one or more) arg 2 - path/to/dir where the outputs will be saved
void	runModule() This method executes the modules primary Java routine.
String	version() Changes to a module class should be accompanied by a increment in version.

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, 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, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, 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.api.ApiModule

getDescription, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

cleanUp, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Constructor Detail

RdpHierParser

public RdpHierParser()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Description copied from class: ScriptModuleImpl

Validate module dependencies:

• Require Config. exists
• Require Config. is positive integer
• Require Config. is positive integer
• Verify Config. is positive integer if set
• Start the AWS DB sync to S3 if a novel DB has been configure and "aws.copyDbToS3" is enabled

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

main

public static void main(String[] args)
                 throws Exception

For stand-alone testing outside of a BioLockJ pipeline.
arg 0 - comma-separated list of taxonomic levels
arg 1 - comma-separated list of input files (one or more)
arg 2 - path/to/dir where the outputs will be saved

Parameters:

args -

Throws:

Exception

runModule

public void runModule()
               throws Exception

Description copied from interface: JavaModule

This method executes the modules primary Java routine.

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

executeTask

public void executeTask()
                 throws Exception

Description copied from class: JavaModuleImpl

JavaModules run pure Java code.
If in Direct mode, execute JavaModuleImpl.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 JavaModuleImpl.runModule() to run the Java code to execute module functionality within the manager instance.

Specified by:

executeTask in interface BioModule

Overrides:

executeTask in class JavaModuleImpl

Throws:

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

getInputFiles

public List<File> getInputFiles()

Description copied from class: BioModuleImpl

BioModule BioModuleImpl.getInputFiles() is called to initialize upon first call and cached.

Specified by:

getInputFiles in interface BioModule

Overrides:

getInputFiles in class BioModuleImpl

Returns:

Input files

isValidInputModule

public boolean isValidInputModule(BioModule module)

Description copied from class: JavaModuleImpl

If module is a SeqModule input must contain sequence data.

Specified by:

isValidInputModule in interface BioModule

Overrides:

isValidInputModule in class JavaModuleImpl

Parameters:

module - BioModule that ran before the current BioModule

Returns:

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

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

Description copied from class: BioModuleImpl

By default, no prerequisites are required.

Specified by:

getPreRequisiteModules in interface BioModule

Overrides:

getPreRequisiteModules in class BioModuleImpl

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getDetails

public String getDetails()

Description copied from interface: ApiModule

A extension of getDescription. Beyond the brief description, give details such as the interaction between properties.

Specified by:

getDetails in interface ApiModule

Overrides:

getDetails in class BioModuleImpl

Returns:

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns:

version

public String version()

Description copied from interface: BioModule

Changes to a module class should be accompanied by a increment in version. The is a string and open form, but using the major.minor.patch semantic versioning is recommended.

Specified by:

version in interface BioModule

Returns: