biolockj.module.hello_world

Class Step3

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.hello_world.Step1

biolockj.module.hello_world.Step2

biolockj.module.hello_world.Step3

All Implemented Interfaces:

ApiModule, BioModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

Step4

public abstract class Step3
extends Step2

Even a very simple module probably uses at least one property. Properties are key/value pairs given in the config file that control what a module does. Its really important to document those! You could just write it all out in your getDetails() method. However is much better to take the time to describe your properties through these ApiModule methods. These methods allow the BioLockJ automated documentation process to generate uniformly formated documentation for all modules, and allows users and GUIs to interact with your module via the command line. There are many properties that your module uses that you have nothing to do with. They are used in methods that are inherited from the parent classes that handle most of the baseline module mechanics. You cover those when you reference super().

Author:

Ivory Blakley

Field Summary

Fields

Modifier and Type	Field and Description
static String	EXCITE_PROP "The number of ! to use with the phrase."
static String	EXCITE_PROP_DESC
static String	NAME_PROP "A name to use instead of \'world\'."; defaults to: "world"
static String	NAME_PROP_DEFAULT
static String	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
Step3()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Be sure to touch any / all properties your module uses.
Boolean	isValidProp(String property) Tests to see if the value val is valid for property prop; primarily tests format.

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, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, 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, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version

Field Detail

NAME_PROP

public static final String NAME_PROP

"A name to use instead of \'world\'."; defaults to: "world"

See Also:

Constant Field Values

NAME_PROP_DESC

public static final String NAME_PROP_DESC

See Also:

Constant Field Values

NAME_PROP_DEFAULT

public static final String NAME_PROP_DEFAULT

See Also:

Constant Field Values

EXCITE_PROP

public static final String EXCITE_PROP

"The number of ! to use with the phrase."

See Also:

Constant Field Values

EXCITE_PROP_DESC

public static final String EXCITE_PROP_DESC

See Also:

Constant Field Values

Constructor Detail

Step3

public Step3()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Be sure to touch any / all properties your module uses. Call your isValidProp(String) method to check individual values. IF applicable, code additional tests here to make sure your properties are compatible.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

isValidProp

public Boolean isValidProp(String property)
                    throws Exception

Description copied from interface: ApiModule

Tests to see if the value val is valid for property prop; primarily tests format. This is designed for individual properties. To make sure property values are compatible, use BioModule.checkDependencies(). Using switch/case or a stack of if/else is recommended. Within each case, call any/all method that is used by this module to access the value from the config file, leveraging the checks in the Config.get* methods. This method should never actually return false. If the value is not valid, it should throw an exception that includes a helpful message about whats not valid. As part of a throwable, that message is passed along to wherever the call started. Any time that "false" is actually the desired form, this method should be wrapped in a try/catch.

Specified by:

isValidProp in interface ApiModule

Overrides:

isValidProp in class ScriptModuleImpl

Returns:

true if value is recognized and good, false/Exception if it is recognized and invalid, null if prop is not recognized.

Throws:

Exception