biolockj.module.hello_world

Class Step4

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.hello_world.Step1

biolockj.module.hello_world.Step2

biolockj.module.hello_world.Step3

biolockj.module.hello_world.Step4

All Implemented Interfaces:

ApiModule, BioModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

Step5

public abstract class Step4
extends Step3

Specify the acceptable input data type for this module. Currently, the way to specify this is through the isValidInputModule method. Test a given module to see if it is an acceptable source of intput data. Your description / details should describe what type of output it makes. Many modules are connected to some other module. They jointly perform a single task, but it still makes sense to break that task into multiple modules. They will reference each as pre- or post-requisite modules.

Author:

Ivory Blakley

Field Summary

Fields inherited from class biolockj.module.hello_world.Step3

EXCITE_PROP, EXCITE_PROP_DESC, NAME_PROP, NAME_PROP_DEFAULT, NAME_PROP_DESC

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
Step4()

Method Summary

Modifier and Type	Method and Description
List<String>	getPostRequisiteModules() By default, no post-requisites are required.
List<String>	getPreRequisiteModules() By default, no prerequisites are required.
boolean	isValidInputModule(BioModule module) In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input.

Methods inherited from class biolockj.module.hello_world.Step3

checkDependencies, isValidProp

Methods inherited from class biolockj.module.hello_world.Step2

getCitationString, getDescription, getDetails

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScript, buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, getWorkerScriptFunctions, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDockerImageOwner, getDockerImageTag, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, 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, listProps

Methods inherited from interface biolockj.module.BioModule

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

Constructor Detail

Step4

public Step4()

Method Detail

getPostRequisiteModules

public List<String> getPostRequisiteModules()
                                     throws Exception

Description copied from class: BioModuleImpl

By default, no post-requisites are required.

Specified by:

getPostRequisiteModules in interface BioModule

Overrides:

getPostRequisiteModules in class BioModuleImpl

Returns:

List of BioModules

Throws:

Exception - if invalid Class names are returned as post-requisites

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

isValidInputModule

public boolean isValidInputModule(BioModule module)

Description copied from class: BioModuleImpl

In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input. This method returns false if the previousModule only produced a new metadata file, such as ImportMetadata or RegisterNumReads. When BioModuleImpl.getInputFiles() is called, this method determines if the previousModule output is valid input for the current BioModule. The default implementation of this method returns FALSE if the previousModule only generates a new metadata file.

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