biolockj.module.hello_world

Class Hello_Friends

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.hello_world.Hello_Friends

All Implemented Interfaces:

ApiModule, BioModule, ScriptModule, Comparable<BioModule>

public class Hello_Friends
extends ScriptModuleImpl
implements ApiModule

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
Hello_Friends()

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() Be sure to touch any / all properties your module uses.
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.
String	getDockerImageName() Get the docker image to use for this module.
List<String>	getWorkerScriptFunctions() Method returns bash script lines used to build the functions called by the worker scripts.
protected String	howExciting() Accesses the "hello.excitmentLevel" and creates a string with that many !s, or just "." if the value is null.
Boolean	isValidProp(String property) Tests to see if the value val is valid for property prop; primarily tests format.
protected String	makeMessage() Create a message based on the modules properties.

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, 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, 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

Hello_Friends

public Hello_Friends()

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

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

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

Description copied from interface: ScriptModule

Method returns bash script lines used to build the functions called by the worker scripts.

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

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, or just "." if the value is null. 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: /:

Specified by:

getDockerImageName in interface BioModule

Returns:

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: