biolockj.module.hello_world

Class Step5

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

biolockj.module.hello_world.Step5

All Implemented Interfaces:

ApiModule, BioModule, ScriptModule, Comparable<BioModule>

public class Step5
extends Step4

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
Step5()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Return an inner list of lines to execute for each sample.
void	checkDependencies() Test anything that might cause your module to fail; especially user input.
String	getDockerImageName() Get the docker image to use for this module.
protected String	howExciting() Accesses the "hello.excitmentLevel" and creates a string with that many !s.
protected String	makeMessage() Create a message based on the modules properties.

Methods inherited from class biolockj.module.hello_world.Step4

getPostRequisiteModules, getPreRequisiteModules, isValidInputModule

Methods inherited from class biolockj.module.hello_world.Step3

isValidProp

Methods inherited from class biolockj.module.hello_world.Step2

getCitationString, getDescription, getDetails

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Constructor Detail

Step5

public Step5()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Test anything that might cause your module to fail; especially user input. In this case, the only problem we foresee is the integer format for one of the properties, which we already check, via super.checkDependencies(); in Step3.checkDependencies() Many modules just check properties for unacceptable values. Some modules may also check than an environment variable is set, or that an executable is reachable, or that some file exists... This check must be reliable and speedy; otherwise it is very open-ended.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class Step3

Throws:

Exception - thrown if missing or invalid dependencies are found

buildScript

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

Description copied from class: ScriptModuleImpl

Return an inner list of lines to execute for each sample. Return these as a list (outer list)

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

makeMessage

protected String makeMessage()
                      throws ConfigFormatException

Create a message based on the modules properties.

Returns:

Throws:

ConfigFormatException

howExciting

protected String howExciting()
                      throws ConfigFormatException

Accesses the "hello.excitmentLevel" and creates a string with that many !s. Notice that this method access the value using the same method that was used in the BioModuleImpl.isValidProp(String)

Returns:

Throws:

ConfigFormatException

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: /:

Returns: